Rationale: This script performs differential gene expression (dge) and calculates the upregulated and downregulated genes in different parts of lichen thallus using Sleuth
1. Prepare data
- list samples to be included
library(sleuth)
library(tidyverse)
samples<-read.delim("../analysis_and_temp_files/03_qc/samples.csv",sep=",")
kal_dirs2 <- data.frame("sample"=samples$run_id, "part"= samples$sample_focus,
substrate=samples$growth_site, thallus = samples$thallus_id,
"path"=paste0("../analysis_and_temp_files/06_meta_mapping/kallisto_meta_mapping/",samples$run_id,"_kallisto")) %>% filter(sample!="MP_I" & sample!="MP_II")
- define list of genes to be included: only mycobiont and only those that have read count across whole panel of >=5
full<-read.delim("../analysis_and_temp_files/08_dge_culture_lichen/counts_table.tsv",row.names=1)
d<-full %>% select(any_of(kal_dirs2$sample)) #include only lichen samples
colnames(d)
## [1] "XBC2" "XBA1" "XSA2_2" "XSC1" "XSE2" "XBE1" "XTA2" "XSC2"
## [9] "XSA2" "XBA2" "XBC1" "XTA1" "XSA1" "XTC2" "XTE2" "XBE2"
## [17] "XMC2"
d$max<-apply(d,1,max)
min(d$max)
## [1] 0
d1<-d[which(d$max>=5),] #to remove lowly expressed genes, keep rows in which max read count across whole panel is atleast 5
# drop the max column, as its not needed anymore
raw_counts<-d1 %>% select(-max)
length(rownames(d1)) # total number of genes
## [1] 11083
length(rownames(raw_counts))
## [1] 11083
#make the list of selected genes
target_id<-rownames(d1)
2. Edge / Center comparison
- read in the data, including only selected genes
- modeled the DGE following the official tutorial
- Produced 7 genes upregulated in center, if we apply the thresholds of qvalue<0.05 and abs(b)>1. No genes upregulated in the edge
ec_dirs<-kal_dirs2 %>% filter(part %in% c("thallus_centre", "thallus_edge") )
ec_dirs$part <- as.factor(ec_dirs$part)
ec_so <- sleuth_prep(ec_dirs,extra_bootstrap_summary = TRUE,filter_target_id = target_id,transformation_function = function(x) log2(x + 0.1))
## Warning in check_num_cores(num_cores): It appears that you are running Sleuth from within Rstudio.
## Because of concerns with forking processes from a GUI, 'num_cores' is being set to 1.
## If you wish to take advantage of multiple cores, please consider running sleuth from the command line.
## reading in kallisto results
## dropping unused factor levels
## ..........
## normalizing est_counts
## A list of target IDs for filtering was found. Using this for filtering
## 11083 targets passed the filter
## normalizing tpm
## merging in metadata
## summarizing bootstraps
## ..........
#model that includes only confounding variables
ec_so <- sleuth_fit(ec_so, ~thallus, 'reduced')
## fitting measurement error models
## shrinkage estimation
## 7 NA values were found during variance shrinkage estimation due to mean observation values outside of the range used for the LOESS fit.
## The LOESS fit will be repeated using exact computation of the fitted surface to extrapolate the missing values.
## These are the target ids with NA values: XANPAGTX0501_000967-T1, XANPAGTX0501_000969-T1, XANPAGTX0501_000980-T1, XANPAGTX0501_002903-T1, XANPAGTX0501_004641-T1, XANPAGTX0501_005100-T1, XANPAGTX0501_006796-T1
## computing variance of betas
#model that includes only both the confounding variable and the variable of interest
ec_so <- sleuth_fit(ec_so, ~thallus + part, 'full')
## fitting measurement error models
## shrinkage estimation
## 7 NA values were found during variance shrinkage estimation due to mean observation values outside of the range used for the LOESS fit.
## The LOESS fit will be repeated using exact computation of the fitted surface to extrapolate the missing values.
## These are the target ids with NA values: XANPAGTX0501_000967-T1, XANPAGTX0501_000969-T1, XANPAGTX0501_000980-T1, XANPAGTX0501_002903-T1, XANPAGTX0501_004641-T1, XANPAGTX0501_005100-T1, XANPAGTX0501_006796-T1
## computing variance of betas
#compare the models
ec_so <- sleuth_lrt(ec_so, 'reduced', 'full')
ec_so <- sleuth_wt(ec_so, 'partthallus_edge')
plot_pca(ec_so, color_by = 'part', text_labels = TRUE,use_filtered=T,units="tpm")

ec_table <- sleuth_results(ec_so, 'partthallus_edge')
ec_sig <- ec_table %>% tibble::as_tibble() %>%
filter( qval <= 0.05, grepl("GTX0501",target_id) ) %>%
arrange(desc(b)) %>% mutate(change = if_else(b > 1, "edge", ifelse(b< -1, "centre", "low_logFC")))
table(ec_sig$change)
##
## centre low_logFC
## 9 170
- Bootstrap of the two genes most overexpressed in the center. The difference isn’t massive
ec_dge<-ec_sig$target_id[ec_sig$change!="low_logFC"]
plot_bootstrap(ec_so,
target_id = ec_dge[7],
units = "est_counts",
color_by = "part")
plot_bootstrap(ec_so,
target_id = ec_dge[6],
units = "est_counts",
color_by = "part")


- About genes upregulated in center, we mostly know nothing. What we do know:
- One secreted
- Two from lichen-enriched orthogroups
- One of them has two InterPro domains: F-box and LRR. This makes it likely to be a part of ubiquitin protein degradation system. F-box connects to the ubiquitin ligase complex, and LRR binds to a specific protein to be degraded (seehttps://www.sciencedirect.com/science/article/pii/S0079610799000103)
library(kableExtra)
funannot2<-read.delim2("../../02_mycobiont_genome/analysis_and_temp_files/09_ortho/lichen_enriched_ortho_in_xanpa.tsv",sep="\t")
center_ec_genes<-ec_sig %>% filter(change=="centre") %>%
left_join(funannot2,by=c("target_id"="TranscriptID")) %>%
select(target_id,b,InterPro_new,CAZyme_new,Protease_new,KO,secreted_consensus,lichen_ortho)
center_ec_genes %>%
kable(format = "html", col.names = colnames(center_ec_genes)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
|
target_id
|
b
|
InterPro_new
|
CAZyme_new
|
Protease_new
|
KO
|
secreted_consensus
|
lichen_ortho
|
|
XANPAGTX0501_005615-T1
|
-1.009109
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005614-T1
|
-1.075863
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008007-T1
|
-1.155943
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002184-T1
|
-1.173653
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001949-T1
|
-1.187615
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002506-T1
|
-1.194636
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008856-T1
|
-1.278297
|
IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_009886-T1
|
-1.292990
|
NA
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_009927-T1
|
-1.619707
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
- This is the gene the closest to being overexpressed in the edge (b value = 0.9).
plot_bootstrap(ec_so,
target_id = ec_sig$target_id[ec_sig$b>0.9],
units = "est_counts",
color_by = "part")

- Interestingly, it’s a putative effector, which is upregulated in lichen and matches papain inhibitor/cellulose-binding
edge_ec_genes<-ec_sig %>% filter(b>0.9) %>%
left_join(funannot2,by=c("target_id"="TranscriptID")) %>%
select(target_id,b,InterPro_new,CAZyme_new,Protease_new,KO,secreted_consensus,lichen_ortho)
edge_ec_genes %>%
kable(format = "html", col.names = colnames(edge_ec_genes)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
|
target_id
|
b
|
InterPro_new
|
CAZyme_new
|
Protease_new
|
KO
|
secreted_consensus
|
lichen_ortho
|
|
XANPAGTX0501_001015-T1
|
0.9022441
|
IPR001153 Barwin domain, IPR009009 RlpA-like protein, double-psi beta-barrel domain, IPR036908 RlpA-like domain superfamily
|
NA
|
NA
|
|
TRUE
|
FALSE
|
2.2. Power analysis: simple
- Do we have enough samples for this comparison?
- Looked at the distribution of (non-corrected) p-values. The graph looks good: close to uniform, with an increase close to 0. If our test was underpowered, we would see an increase of p-vlaues along 0->1, but this is not the case
ggplot(ec_table)+geom_histogram(aes(x=pval))
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
## Warning: Removed 690798 rows containing non-finite values (`stat_bin()`).

library(MKpower)
qqunif(ec_table$pval, color.line = "orange")

- However, when looking at corrected p-values (a.k.a. q-values), the graph looks bad
ggplot(ec_table)+geom_histogram(aes(x=qval))
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
## Warning: Removed 690798 rows containing non-finite values (`stat_bin()`).
* Perhaps, this particular comparison is underpowered
library(MKpower)
qqunif(ec_table$qval, color.line = "orange")

3. Center / apothetia comparison
- Only 1 gene upregulated in the center compared to 118 in apothecia
ca_dirs<-kal_dirs2 %>% filter(part %in% c("thallus_centre", "apothecia") )
ca_dirs$part <- as.factor(ca_dirs$part)
ca_dirs$thallus<- as.factor(ca_dirs$thallus)
rhdf5::h5closeAll()
ca_so <- sleuth_prep(ca_dirs,extra_bootstrap_summary = TRUE,filter_target_id = target_id,transformation_function = function(x) log2(x + 0.1))
## Warning in check_num_cores(num_cores): It appears that you are running Sleuth from within Rstudio.
## Because of concerns with forking processes from a GUI, 'num_cores' is being set to 1.
## If you wish to take advantage of multiple cores, please consider running sleuth from the command line.
## reading in kallisto results
## dropping unused factor levels
## .............
## normalizing est_counts
## A list of target IDs for filtering was found. Using this for filtering
## 11083 targets passed the filter
## normalizing tpm
## merging in metadata
## summarizing bootstraps
## .............
#model that includes only confounding variables
ca_so <- sleuth_fit(ca_so, ~thallus, 'reduced')
## fitting measurement error models
## shrinkage estimation
## 2 NA values were found during variance shrinkage estimation due to mean observation values outside of the range used for the LOESS fit.
## The LOESS fit will be repeated using exact computation of the fitted surface to extrapolate the missing values.
## These are the target ids with NA values: XANPAGTX0501_004237-T1, XANPAGTX0501_010518-T1
## computing variance of betas
#model that includes only both the confounding variable and the variable of interest
ca_so <- sleuth_fit(ca_so, ~thallus + part, 'full')
## fitting measurement error models
## shrinkage estimation
## 3 NA values were found during variance shrinkage estimation due to mean observation values outside of the range used for the LOESS fit.
## The LOESS fit will be repeated using exact computation of the fitted surface to extrapolate the missing values.
## These are the target ids with NA values: XANPAGTX0501_004237-T1, XANPAGTX0501_010518-T1, XANPAGTX0501_010086-T1
## computing variance of betas
#compare the models
ca_so <- sleuth_lrt(ca_so, 'reduced', 'full')
ca_so <- sleuth_wt(ca_so, 'partthallus_centre')
plot_pca(ca_so, color_by = 'part', text_labels = TRUE,use_filtered=T,units="tpm")

ca_table <- sleuth_results(ca_so, 'partthallus_centre')
ca_sig <- ca_table %>% tibble::as_tibble() %>%
filter( qval <= 0.05, grepl("GTX0501",target_id) ) %>%
arrange(desc(b)) %>% mutate(change = if_else(b > 1, "centre", ifelse(b< -1, "apothecium", "low_logFC")))
table(ca_sig$change)
##
## apothecium centre low_logFC
## 118 1 1928
Upregulated in apothecia
- Bootstrap of the two genes most overexpressed in the apothecium. Why are the boxes so wide?
plot_bootstrap(ca_so,
target_id = ca_sig$target_id[which.min(ca_sig$b)],
units = "est_counts",
color_by = "part")
plot_bootstrap(ca_so,
target_id = ca_sig$target_id[which.min(ca_sig$b[-which.min(ca_sig$b)])],
units = "est_counts",
color_by = "part")


- Both MAT genes seem upregulated, although XANPAGTX0501_002103-T1 is just below the threshold -0.99
plot_bootstrap(ca_so,
target_id = "XANPAGTX0501_002103-T1",
units = "est_counts",
color_by = "part")
plot_bootstrap(ca_so,
target_id = "XANPAGTX0501_002104-T1",
units = "est_counts",
color_by = "part")


- Of the 118 upregulated in apothecia, 87 have no functional annotations
- 9 are secreted
ap_ca_genes<-ca_sig %>% filter(change=="apothecium") %>%
left_join(funannot2,by=c("target_id"="TranscriptID")) %>%
select(target_id,b,InterPro_new,CAZyme_new,Protease_new,KO,secreted_consensus,lichen_ortho)
ap_ca_genes %>%
kable(format = "html", col.names = colnames(ap_ca_genes)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
|
target_id
|
b
|
InterPro_new
|
CAZyme_new
|
Protease_new
|
KO
|
secreted_consensus
|
lichen_ortho
|
|
XANPAGTX0501_001605-T1
|
-1.002217
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004628-T1
|
-1.002890
|
IPR002156 Ribonuclease H domain, IPR012337 Ribonuclease H-like superfamily, IPR036397 Ribonuclease H superfamily
|
NA
|
NA
|
K03469
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009621-T1
|
-1.004737
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008874-T1
|
-1.005597
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_007403-T1
|
-1.005610
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_004416-T1
|
-1.006355
|
IPR000246 Peptidase T2, asparaginase 2, IPR029055 Nucleophile aminohydrolases, N-terminal, IPR037464 Threonine aspartase 1
|
NA
|
T02
|
K08657
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009141-T1
|
-1.008026
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002166-T1
|
-1.010246
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_003282-T1
|
-1.010415
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006245-T1
|
-1.011007
|
NA
|
NA
|
NA
|
|
TRUE
|
TRUE
|
|
XANPAGTX0501_001082-T1
|
-1.011584
|
IPR004853 Sugar phosphate transporter domain
|
NA
|
NA
|
K26222
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002170-T1
|
-1.014622
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002104-T1
|
-1.017319
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002183-T1
|
-1.017368
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004494-T1
|
-1.018387
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_007464-T1
|
-1.021451
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005615-T1
|
-1.022220
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001888-T1
|
-1.023478
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005658-T1
|
-1.031831
|
IPR001153 Barwin domain, IPR009009 RlpA-like protein, double-psi beta-barrel domain, IPR036908 RlpA-like domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002163-T1
|
-1.035184
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008533-T1
|
-1.037400
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009317-T1
|
-1.039048
|
IPR008979 Galactose-binding-like domain superfamily
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_005061-T1
|
-1.045582
|
NA
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_001947-T1
|
-1.046488
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004580-T1
|
-1.050842
|
IPR007292 Nuclear fusion protein Kar5
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006974-T1
|
-1.052396
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002057-T1
|
-1.052723
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006203-T1
|
-1.055462
|
IPR001841 Zinc finger, RING-type, IPR002867 IBR domain, IPR013083 Zinc finger, RING/FYVE/PHD-type, IPR017907 Zinc finger, RING-type, conserved site
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002184-T1
|
-1.055941
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001330-T1
|
-1.062267
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_004493-T1
|
-1.069215
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005597-T1
|
-1.070417
|
IPR006421 Glycogen debranching enzyme, metazoa, IPR008928 Six-hairpin glycosidase superfamily, IPR012341 Six-hairpin glycosidase-like superfamily, IPR017853 Glycoside hydrolase superfamily, IPR029436 Eukaryotic glycogen debranching enzyme, N-terminal domain, IPR032788 Glycogen debranching enzyme, central domain, IPR032790 Glycogen debranching enzyme, C-terminal, IPR032792 Glycogen debranching enzyme, glucanotransferase domain
|
GH133
|
NA
|
K01196
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008628-T1
|
-1.071911
|
IPR023346 Lysozyme-like domain superfamily
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_003775-T1
|
-1.074091
|
IPR003100 PAZ domain, IPR003165 Piwi domain, IPR012337 Ribonuclease H-like superfamily, IPR014811 Argonaute, linker 1 domain, IPR032472 Argonaute linker 2 domain, IPR032473 Protein argonaute, Mid domain, IPR032474 Protein argonaute, N-terminal, IPR036085 PAZ domain superfamily, IPR036397 Ribonuclease H superfamily
|
NA
|
NA
|
K11593
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000647-T1
|
-1.082215
|
IPR000571 Zinc finger, CCCH-type
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006255-T1
|
-1.084624
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_010303-T1
|
-1.086556
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004891-T1
|
-1.088838
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000681-T1
|
-1.089087
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001010-T1
|
-1.089790
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004217-T1
|
-1.090288
|
IPR000504 RNA recognition motif domain, IPR012677 Nucleotide-binding alpha-beta plait domain superfamily, IPR035979 RNA-binding domain superfamily
|
NA
|
NA
|
K24990
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001436-T1
|
-1.091349
|
IPR002048 EF-hand domain, IPR011992 EF-hand domain pair, IPR018247 EF-Hand 1, calcium-binding site
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006910-T1
|
-1.092752
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_007871-T1
|
-1.093262
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_000005-T1
|
-1.100476
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009139-T1
|
-1.106326
|
IPR001876 Zinc finger, RanBP2-type
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001333-T1
|
-1.109653
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_003212-T1
|
-1.110801
|
IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily, IPR036047 F-box-like domain superfamily
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_008009-T1
|
-1.110995
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006016-T1
|
-1.111020
|
IPR008928 Six-hairpin glycosidase superfamily, IPR031335 Glycosyl hydrolase family 63, C-terminal
|
GH63
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008008-T1
|
-1.111120
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006330-T1
|
-1.113100
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004104-T1
|
-1.113445
|
IPR001214 SET domain, IPR011990 Tetratricopeptide-like helical domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001362-T1
|
-1.113981
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001951-T1
|
-1.118810
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005630-T1
|
-1.120143
|
IPR036928 Amidase signature (AS) superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008534-T1
|
-1.122508
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000025-T1
|
-1.123779
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_004950-T1
|
-1.124212
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002522-T1
|
-1.132906
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_003572-T1
|
-1.135075
|
IPR001087 GDSL lipase/esterase, IPR036514 SGNH hydrolase superfamily
|
CE16
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_007067-T1
|
-1.135736
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_007234-T1
|
-1.142869
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_007262-T1
|
-1.143084
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_010203-T1
|
-1.143084
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_005279-T1
|
-1.148052
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_010380-T1
|
-1.148975
|
IPR000210 BTB/POZ domain, IPR011333 SKP1/BTB/POZ domain superfamily
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_010007-T1
|
-1.149075
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009615-T1
|
-1.156978
|
IPR035940 CAP superfamily
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_002172-T1
|
-1.161670
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_003209-T1
|
-1.170208
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008041-T1
|
-1.181328
|
NA
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_001910-T1
|
-1.190522
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009318-T1
|
-1.192876
|
IPR011333 SKP1/BTB/POZ domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004521-T1
|
-1.198724
|
IPR008271 Serine/threonine-protein kinase, active site, IPR011009 Protein kinase-like domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001612-T1
|
-1.207043
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_010304-T1
|
-1.207964
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001538-T1
|
-1.211841
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009602-T1
|
-1.212068
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008007-T1
|
-1.213991
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008782-T1
|
-1.216240
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006951-T1
|
-1.222177
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005402-T1
|
-1.225284
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_001414-T1
|
-1.228686
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000194-T1
|
-1.233329
|
IPR006047 Glycosyl hydrolase, family 13, catalytic domain, IPR013780 Glycosyl hydrolase, all-beta, IPR017853 Glycoside hydrolase superfamily
|
GH13
|
NA
|
K01176
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005766-T1
|
-1.254576
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009582-T1
|
-1.264645
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005735-T1
|
-1.281286
|
IPR018824 Conidiation-specific protein 6
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008331-T1
|
-1.288651
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001611-T1
|
-1.298257
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_007900-T1
|
-1.308741
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_008090-T1
|
-1.312749
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002182-T1
|
-1.314625
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009619-T1
|
-1.314627
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008284-T1
|
-1.314835
|
IPR029044 Nucleotide-diphospho-sugar transferases
|
GT2_Glyco_tranf_2
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004520-T1
|
-1.321604
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001963-T1
|
-1.324243
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001960-T1
|
-1.329881
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000193-T1
|
-1.344509
|
IPR006047 Glycosyl hydrolase, family 13, catalytic domain, IPR017853 Glycoside hydrolase superfamily
|
GH13
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001967-T1
|
-1.356557
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001063-T1
|
-1.359981
|
NA
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_001856-T1
|
-1.377390
|
IPR037176 Osmotin/thaumatin-like superfamily
|
NA
|
NA
|
|
TRUE
|
TRUE
|
|
XANPAGTX0501_002506-T1
|
-1.384452
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006327-T1
|
-1.392539
|
IPR018466 Yeast cell wall synthesis Kre9/Knh1-like, N-terminal
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_007397-T1
|
-1.396019
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_007872-T1
|
-1.413947
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_010596-T1
|
-1.414271
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008420-T1
|
-1.415724
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000892-T1
|
-1.427350
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000378-T1
|
-1.444983
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_003211-T1
|
-1.502300
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_010280-T1
|
-1.533833
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005814-T1
|
-1.541250
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009786-T1
|
-1.554050
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009926-T1
|
-1.646262
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004966-T1
|
-1.664164
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008109-T1
|
-2.657633
|
IPR004143 Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain
|
NA
|
NA
|
K03800
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001156-T3
|
-3.910405
|
IPR003822 Paired amphipathic helix, IPR013194 Histone deacetylase interacting domain, IPR031693 Sin3, C-terminal, IPR036600 Paired amphipathic helix superfamily
|
NA
|
NA
|
K11644
|
FALSE
|
FALSE
|
- Selected only genes that are potentially multicellularity related
mult_list<-read.delim2("../analysis_and_temp_files/08_dge_culture_lichen/multicellularity.txt")
#select genes that come from one of the categories of interest
ips_df <-funannot2 %>% select(TranscriptID,InterPro_new) %>%
mutate(InterPro_new = strsplit(InterPro_new, ", I")) %>%
unnest(InterPro_new) %>% mutate(InterPro_new=str_replace(InterPro_new,"^PR","IPR")) %>%
mutate(short_term = substr(InterPro_new, 1,40))
ips_selected<-ips_df %>% mutate(ID=gsub( " .*$", "", InterPro_new)) %>% inner_join(mult_list,relationship = "many-to-many") %>% select(-c(InterPro_new,short_term))
## Joining with `by = join_by(ID)`
ko_cazy_selected<-funannot2 %>% select(TranscriptID,KO,CAZyme_new) %>%
pivot_longer(-TranscriptID,names_to = "Annotation",values_to = "ID") %>% inner_join(mult_list,relationship = "many-to-many") %>% select(-Annotation)
## Joining with `by = join_by(ID)`
mult_gene_table<-rbind(ips_selected,ko_cazy_selected)
mult_gene_table_ap<-mult_gene_table %>% inner_join(ca_sig %>% filter(change=="apothecium") %>% select(target_id,b),by=c("TranscriptID"="target_id")) %>% arrange(Function)
mult_gene_table_ap %>%
kable(format = "html", col.names = colnames(mult_gene_table_ap)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
|
TranscriptID
|
ID
|
Annotation_type
|
Description
|
Function
|
Function_type
|
b
|
|
XANPAGTX0501_005597-T1
|
IPR032788
|
IPR
|
Glycogen debranching enzyme, central domain
|
Carbohydrate storage
|
Fungal multicellularity
|
-1.070417
|
|
XANPAGTX0501_000647-T1
|
IPR000571
|
IPR
|
Zinc finger, CCCH-type
|
Cell division, proliferation and growth
|
Fungal multicellularity
|
-1.082215
|
|
XANPAGTX0501_003775-T1
|
IPR012337
|
IPR
|
Ribonuclease H-like superfamily
|
Cell division, proliferation and growth
|
Fungal multicellularity
|
-1.074091
|
|
XANPAGTX0501_004104-T1
|
IPR001214
|
IPR
|
SET domain
|
Cell division, proliferation and growth
|
Fungal multicellularity
|
-1.113445
|
|
XANPAGTX0501_004628-T1
|
IPR012337
|
IPR
|
Ribonuclease H-like superfamily
|
Cell division, proliferation and growth
|
Fungal multicellularity
|
-1.002890
|
|
XANPAGTX0501_005735-T1
|
IPR018824
|
IPR
|
Conidiation-specific protein 6
|
Cell surface and cell wall proteins
|
Fungal multicellularity
|
-1.281286
|
|
XANPAGTX0501_006327-T1
|
IPR018466
|
IPR
|
Yeast cell wall synthesis Kre9/Knh1-like, N-terminal
|
Cell wall biosynthesis
|
Fungal multicellularity
|
-1.392539
|
|
XANPAGTX0501_001856-T1
|
IPR037176
|
IPR
|
Osmotin/thaumatin-like superfamily
|
Cell wall remodeling
|
Fungal multicellularity
|
-1.377390
|
|
XANPAGTX0501_003212-T1
|
IPR001810
|
IPR
|
F-box domain
|
Protein ubiquitination
|
Fungal multicellularity
|
-1.110801
|
|
XANPAGTX0501_006203-T1
|
IPR017907
|
IPR
|
Zinc finger; RING-type; conserved site
|
Protein ubiquitination
|
Fungal multicellularity
|
-1.055462
|
|
XANPAGTX0501_010380-T1
|
IPR000210
|
IPR
|
BTB/POZ domain
|
Protein ubiquitination
|
Fungal multicellularity
|
-1.148975
|
|
XANPAGTX0501_004217-T1
|
IPR000504
|
IPR
|
RNA recognition motif domain
|
RNA binding proteins
|
Expression regulation
|
-1.090288
|
|
XANPAGTX0501_003775-T1
|
IPR032474
|
IPR
|
Protein argonaute, N-terminal
|
RNA interference
|
Expression regulation
|
-1.074091
|
|
XANPAGTX0501_006203-T1
|
IPR013083
|
IPR
|
Zinc finger, RING/FYVE/PHD-type
|
Transcription factors
|
Expression regulation
|
-1.055462
|
- Other notable proteins:
- Another protein from ubiquitin degrading system with a F-box and LRR domains
- Multiple transcription factors with different Zinc finger domains and IPR000210 BTB/POZ domain
- IPR031693 Sin3, C-terminal, which is a transcriptional repressor
- IPR018824 Conidiation-specific protein 6, function unknown
- Secreted IPR035940 CAP superfamily protein (egulation of extracellular matrix and branching morphogenesis, either proteases or protease inhibitors)
- Several GHs
- InterPro enrichement analysis
###make table with IPS annotations
ips_df <-funannot2 %>% select(TranscriptID,InterPro_new) %>%
mutate(InterPro_new = strsplit(InterPro_new, ", I")) %>%
unnest(InterPro_new) %>% mutate(InterPro_new=str_replace(InterPro_new,"^PR","IPR")) %>%
mutate(short_term = substr(InterPro_new, 1,40))
ips_data <- list(
term2protein = data.frame(
term = ips_df$InterPro_new,
gene = ips_df$TranscriptID
),
term2name = data.frame(
term = ips_df$InterPro_new,
name = ips_df$short_term
),
universe = unique(as.character(ips_df$TranscriptID))
)
###enrichment analysis
enrich<-clusterProfiler::enricher(ap_ca_genes$target_id,
pAdjustMethod = "none",
minGSSize = 1,
maxGSSize = 2000,
qvalueCutoff = 1,
universe=ips_data$universe,
TERM2GENE=ips_data$term2protein,
TERM2NAME=ips_data$term2name)
enrich_pairwise<-enrichplot::pairwise_termsim(enrich)
enrichplot::emapplot(enrich_pairwise)

The only gene showed as upregulated in center.
- This gene is expressed in most samples, but there is a high level of heterogeneity across different lichen individuals, obscuring the pattern of it being more highly expressed in the center
plot_bootstrap(ca_so,
target_id = ca_sig$target_id[which.max(ca_sig$b)],
units = "est_counts",
color_by = "part")

- This is the second, which is just below the threshold (b = 0.98)
plot_bootstrap(ca_so,
target_id = "XANPAGTX0501_004633-T1",
units = "est_counts",
color_by = "part")

- Nothing is known about either!
ce_ca_genes<-ca_sig %>% filter(b>0.9) %>%
left_join(funannot2,by=c("target_id"="TranscriptID")) %>%
select(target_id,b,InterPro_new,CAZyme_new,Protease_new,KO,secreted_consensus,lichen_ortho)
ce_ca_genes %>%
kable(format = "html", col.names = colnames(ce_ca_genes)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
|
target_id
|
b
|
InterPro_new
|
CAZyme_new
|
Protease_new
|
KO
|
secreted_consensus
|
lichen_ortho
|
|
XANPAGTX0501_006303-T1
|
1.3084877
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_004633-T1
|
0.9765075
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
3.2. Power analysis: simple
- Do we have enough samples for this comparison?
- Looked at the distribution of corrected p-values (a.k.a. q-values). The graph looks good: close to uniform, with an increase close to 0. If our test was underpowered, we would see an increase of p-vlaues along 0->1, but this is not the case
ggplot(ca_table)+geom_histogram(aes(x=qval))
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
## Warning: Removed 690798 rows containing non-finite values (`stat_bin()`).

library(MKpower)
qqunif(ca_table$qval, color.line = "orange")

4. Edge / apothetia comparison
- Only 1 gene upregulated in the center compared to 118 in apothecia
ea_dirs<-kal_dirs2 %>% filter(part %in% c("thallus_edge", "apothecia") )
ea_dirs$part <- as.factor(ea_dirs$part)
ea_dirs$thallus<- as.factor(ea_dirs$thallus)
rhdf5::h5closeAll()
ea_so <- sleuth_prep(ea_dirs,extra_bootstrap_summary = TRUE,filter_target_id = target_id,transformation_function = function(x) log2(x + 0.1))
## Warning in check_num_cores(num_cores): It appears that you are running Sleuth from within Rstudio.
## Because of concerns with forking processes from a GUI, 'num_cores' is being set to 1.
## If you wish to take advantage of multiple cores, please consider running sleuth from the command line.
## reading in kallisto results
## dropping unused factor levels
## ...........
## normalizing est_counts
## A list of target IDs for filtering was found. Using this for filtering
## 11083 targets passed the filter
## normalizing tpm
## merging in metadata
## summarizing bootstraps
## ...........
#model that includes only confounding variables
ea_so <- sleuth_fit(ea_so, ~thallus, 'reduced')
## fitting measurement error models
## shrinkage estimation
## computing variance of betas
#model that includes only both the confounding variable and the variable of interest
ea_so <- sleuth_fit(ea_so, ~ thallus + part, 'full')
## fitting measurement error models
## shrinkage estimation
## 1 NA values were found during variance shrinkage estimation due to mean observation values outside of the range used for the LOESS fit.
## The LOESS fit will be repeated using exact computation of the fitted surface to extrapolate the missing values.
## These are the target ids with NA values: XANPAGTX0501_010086-T1
## computing variance of betas
#compare the models
ea_so <- sleuth_lrt(ea_so, 'reduced', 'full')
ea_so <- sleuth_wt(ea_so, 'partthallus_edge')
ea_table <- sleuth_results(ea_so, 'partthallus_edge')
ea_sig <- ea_table %>% tibble::as_tibble() %>%
filter( qval <= 0.05, grepl("GTX0501",target_id) ) %>%
arrange(desc(b)) %>% mutate(change = if_else(b > 1, "edge", ifelse(b< -1, "apothecium", "low_logFC")))
plot_pca(ea_so, color_by = 'part', text_labels = TRUE,use_filtered=T,units="tpm")

table(ea_sig$change)
##
## apothecium edge low_logFC
## 371 13 1772
Upregulated in apothecia
- Bootstrap of the two genes most overexpressed in the apothecium.
plot_bootstrap(ea_so,
target_id = ea_sig$target_id[which.min(ea_sig$b)],
units = "est_counts",
color_by = "part")
plot_bootstrap(ea_so,
target_id = ea_sig$target_id[which.min(ea_sig$b[-which.min(ea_sig$b)])],
units = "est_counts",
color_by = "part")


- Both MAT genes seem upregulated, with b-value of -1.8
plot_bootstrap(ea_so,
target_id = "XANPAGTX0501_002103-T1",
units = "est_counts",
color_by = "part")
plot_bootstrap(ea_so,
target_id = "XANPAGTX0501_002104-T1",
units = "est_counts",
color_by = "part")


- Of the 371 upregulated in apothecia, 255 have no functional annotations
- 33 are secreted
ap_ea_genes<-ea_sig %>% filter(change=="apothecium") %>%
left_join(funannot2,by=c("target_id"="TranscriptID")) %>%
select(target_id,b,InterPro_new,CAZyme_new,Protease_new,KO,secreted_consensus,lichen_ortho)
ap_ea_genes %>%
kable(format = "html", col.names = colnames(ap_ea_genes)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
|
target_id
|
b
|
InterPro_new
|
CAZyme_new
|
Protease_new
|
KO
|
secreted_consensus
|
lichen_ortho
|
|
XANPAGTX0501_006767-T1
|
-1.001121
|
IPR017956 AT hook, DNA-binding motif
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001647-T1
|
-1.003441
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006026-T1
|
-1.005997
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_010639-T1
|
-1.009995
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_000350-T1
|
-1.010205
|
IPR003439 ABC transporter-like, ATP-binding domain, IPR003593 AAA+ ATPase domain, IPR013525 ABC-2 type transporter, IPR017871 ABC transporter-like, conserved site, IPR027417 P-loop containing nucleoside triphosphate hydrolase
|
NA
|
NA
|
K05681
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005347-T1
|
-1.010680
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004759-T1
|
-1.011221
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006900-T1
|
-1.012780
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009389-T1
|
-1.014539
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_007378-T1
|
-1.016970
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005621-T1
|
-1.020780
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_010022-T1
|
-1.023610
|
NA
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_009499-T1
|
-1.023663
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006945-T1
|
-1.030462
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000661-T1
|
-1.032709
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_006946-T1
|
-1.037233
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002624-T1
|
-1.038299
|
IPR029058 Alpha/Beta hydrolase fold
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_010094-T1
|
-1.039693
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008594-T1
|
-1.040188
|
IPR036259 MFS transporter superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001497-T1
|
-1.040517
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000203-T1
|
-1.040557
|
IPR001938 Thaumatin family, IPR037176 Osmotin/thaumatin-like superfamily
|
GH152
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_010087-T1
|
-1.040935
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_003186-T1
|
-1.041709
|
NA
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_010640-T1
|
-1.042747
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004003-T1
|
-1.043412
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000909-T1
|
-1.050406
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002181-T1
|
-1.050504
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_010204-T1
|
-1.051517
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_006142-T1
|
-1.056449
|
NA
|
NA
|
NA
|
|
TRUE
|
TRUE
|
|
XANPAGTX0501_005447-T1
|
-1.060382
|
IPR024500 Domain of unknown function DUF3074
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004484-T1
|
-1.063011
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_000065-T1
|
-1.064314
|
IPR027921 NOP protein chaperone 1
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006920-T1
|
-1.066060
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_003265-T1
|
-1.067945
|
IPR007203 ORMDL family
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002152-T1
|
-1.069475
|
IPR027417 P-loop containing nucleoside triphosphate hydrolase, IPR040632 Sulfotransferase, S. mansonii-type
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_003742-T1
|
-1.069824
|
IPR001509 NAD-dependent epimerase/dehydratase, IPR036291 NAD(P)-binding domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006931-T1
|
-1.072494
|
IPR013087 Zinc finger C2H2-type
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002657-T1
|
-1.073491
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005924-T1
|
-1.074455
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_007353-T1
|
-1.077217
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_005583-T1
|
-1.079779
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009580-T1
|
-1.091993
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004141-T1
|
-1.102317
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_010231-T1
|
-1.104490
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008637-T1
|
-1.106264
|
NA
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_000885-T1
|
-1.108859
|
IPR036305 RGS domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_003865-T1
|
-1.109235
|
NA
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_000417-T1
|
-1.109737
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005025-T1
|
-1.115496
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000848-T1
|
-1.115545
|
IPR016137 RGS domain, IPR036305 RGS domain superfamily
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_006384-T1
|
-1.125655
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004308-T1
|
-1.127582
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_010011-T1
|
-1.134493
|
IPR036013 Band 7/SPFH domain superfamily
|
NA
|
NA
|
K07192
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005047-T1
|
-1.135514
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002639-T1
|
-1.136570
|
IPR002740 EVE domain, IPR015947 PUA-like superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006342-T1
|
-1.138964
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_004244-T1
|
-1.139706
|
IPR003165 Piwi domain, IPR012337 Ribonuclease H-like superfamily, IPR014811 Argonaute, linker 1 domain, IPR032472 Argonaute linker 2 domain, IPR032474 Protein argonaute, N-terminal, IPR036085 PAZ domain superfamily, IPR036397 Ribonuclease H superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005153-T1
|
-1.141212
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009787-T1
|
-1.141882
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008527-T1
|
-1.142627
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009812-T1
|
-1.143459
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006215-T1
|
-1.145166
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001925-T1
|
-1.145918
|
IPR001841 Zinc finger, RING-type, IPR002867 IBR domain
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006992-T1
|
-1.146775
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_010010-T1
|
-1.146789
|
IPR036013 Band 7/SPFH domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009594-T1
|
-1.149357
|
IPR002877 Ribosomal RNA methyltransferase, FtsJ domain, IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005832-T1
|
-1.150654
|
IPR009836 Glycine-rich domain-containing protein-like
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006250-T1
|
-1.153982
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002478-T1
|
-1.154555
|
IPR013126 Heat shock protein 70 family, IPR043129 ATPase, nucleotide binding domain
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_003033-T1
|
-1.155116
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002477-T1
|
-1.157099
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_010530-T1
|
-1.158664
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001222-T1
|
-1.167774
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009738-T1
|
-1.170585
|
IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily, IPR036047 F-box-like domain superfamily
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_006766-T1
|
-1.171555
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_010007-T1
|
-1.175289
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009438-T1
|
-1.175488
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_003238-T1
|
-1.177022
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009437-T1
|
-1.179555
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_010368-T1
|
-1.180001
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001509-T1
|
-1.181146
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001462-T1
|
-1.182311
|
IPR008775 Phytanoyl-CoA dioxygenase-like
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_005177-T1
|
-1.185673
|
IPR001313 Pumilio RNA-binding repeat, IPR011989 Armadillo-like helical, IPR016024 Armadillo-type fold, IPR033133 Pumilio homology domain, IPR033712 Pumilio, RNA binding domain
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001839-T1
|
-1.189988
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009785-T1
|
-1.191020
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_007467-T1
|
-1.203546
|
IPR013830 SGNH hydrolase-type esterase domain, IPR036514 SGNH hydrolase superfamily
|
CE3
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_010638-T1
|
-1.203845
|
IPR003593 AAA+ ATPase domain, IPR003959 ATPase, AAA-type, core, IPR027417 P-loop containing nucleoside triphosphate hydrolase
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_008862-T1
|
-1.204663
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008420-T1
|
-1.205385
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_010529-T1
|
-1.212807
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_001648-T1
|
-1.214948
|
IPR000504 RNA recognition motif domain, IPR012677 Nucleotide-binding alpha-beta plait domain superfamily, IPR035979 RNA-binding domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005677-T1
|
-1.220573
|
IPR004313 Acireductone dioxygenase ARD family, IPR011051 RmlC-like cupin domain superfamily, IPR014710 RmlC-like jelly roll fold, IPR027496 Acireductone dioxygenase, eukaryotes
|
NA
|
NA
|
K08967
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005317-T1
|
-1.226163
|
NA
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_005370-T1
|
-1.231519
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000888-T1
|
-1.234664
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009407-T1
|
-1.241242
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009599-T1
|
-1.242828
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006143-T1
|
-1.243856
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000622-T1
|
-1.244489
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_007851-T1
|
-1.245823
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001498-T1
|
-1.248272
|
IPR012340 Nucleic acid-binding, OB-fold
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008005-T1
|
-1.251448
|
IPR001965 Zinc finger, PHD-type, IPR011011 Zinc finger, FYVE/PHD-type, IPR013083 Zinc finger, RING/FYVE/PHD-type, IPR019786 Zinc finger, PHD-type, conserved site, IPR019787 Zinc finger, PHD-finger
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005952-T1
|
-1.253184
|
IPR032675 Leucine-rich repeat domain superfamily
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_000707-T1
|
-1.255320
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_003775-T2
|
-1.260916
|
IPR003100 PAZ domain, IPR003165 Piwi domain, IPR012337 Ribonuclease H-like superfamily, IPR014811 Argonaute, linker 1 domain, IPR032472 Argonaute linker 2 domain, IPR032473 Protein argonaute, Mid domain, IPR032474 Protein argonaute, N-terminal, IPR036085 PAZ domain superfamily, IPR036397 Ribonuclease H superfamily
|
NA
|
NA
|
K11593
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005280-T1
|
-1.264296
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_003264-T1
|
-1.264968
|
IPR000210 BTB/POZ domain, IPR011333 SKP1/BTB/POZ domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008708-T1
|
-1.265455
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001062-T1
|
-1.268232
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_006095-T1
|
-1.272978
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009628-T1
|
-1.276921
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004596-T1
|
-1.281428
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004753-T1
|
-1.281897
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000281-T1
|
-1.282182
|
IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_003198-T1
|
-1.286713
|
IPR022085 Oxopyrrolidines biosynthesis cluster protein G
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_010276-T1
|
-1.289004
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_010523-T1
|
-1.289004
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_007934-T1
|
-1.291157
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002054-T1
|
-1.291837
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_005550-T1
|
-1.294683
|
IPR001810 F-box domain, IPR036047 F-box-like domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005188-T1
|
-1.298616
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004102-T1
|
-1.299115
|
IPR000420 Yeast PIR protein repeat
|
NA
|
NA
|
K26550
|
TRUE
|
FALSE
|
|
XANPAGTX0501_002019-T1
|
-1.299594
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_010021-T1
|
-1.299618
|
NA
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_002159-T1
|
-1.301773
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_002946-T1
|
-1.307564
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_003790-T1
|
-1.311097
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_002123-T1
|
-1.312729
|
IPR000504 RNA recognition motif domain, IPR007855 RNA-dependent RNA polymerase, eukaryotic-type, IPR035979 RNA-binding domain superfamily
|
NA
|
NA
|
K11699
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000751-T1
|
-1.312812
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001644-T1
|
-1.313601
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_007232-T1
|
-1.314325
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006139-T1
|
-1.315900
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001436-T1
|
-1.320276
|
IPR002048 EF-hand domain, IPR011992 EF-hand domain pair, IPR018247 EF-Hand 1, calcium-binding site
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006420-T1
|
-1.320799
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005281-T1
|
-1.324225
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004466-T1
|
-1.328900
|
IPR000490 Glycoside hydrolase family 17, IPR017853 Glycoside hydrolase superfamily, IPR018620 Ubiquitin 3 binding protein But2, C-terminal
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_002098-T1
|
-1.334348
|
IPR000504 RNA recognition motif domain, IPR012677 Nucleotide-binding alpha-beta plait domain superfamily, IPR035979 RNA-binding domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_007833-T1
|
-1.343993
|
IPR002889 Carbohydrate-binding WSC, IPR018535 Domain of unknown function DUF1996
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004270-T1
|
-1.346903
|
IPR009465 Spondin, N-terminal
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_003124-T1
|
-1.348872
|
IPR001461 Aspartic peptidase A1 family, IPR001969 Aspartic peptidase, active site, IPR021109 Aspartic peptidase domain superfamily, IPR033121 Peptidase family A1 domain, IPR034164 Pepsin-like domain
|
NA
|
A01A
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_000938-T1
|
-1.358336
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_007254-T1
|
-1.362647
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_010211-T1
|
-1.362647
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008200-T1
|
-1.362879
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_003864-T1
|
-1.363940
|
IPR009075 Acyl-CoA dehydrogenase/oxidase C-terminal, IPR009100 Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily, IPR013786 Acyl-CoA dehydrogenase/oxidase, N-terminal, IPR036250 Acyl-CoA dehydrogenase-like, C-terminal, IPR037069 Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005775-T1
|
-1.364250
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_007473-T1
|
-1.375934
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_007936-T1
|
-1.379176
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005640-T1
|
-1.380432
|
IPR013087 Zinc finger C2H2-type
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_000026-T1
|
-1.381814
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_010180-T1
|
-1.383532
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_010275-T1
|
-1.384204
|
IPR003593 AAA+ ATPase domain, IPR027417 P-loop containing nucleoside triphosphate hydrolase, IPR041679 DNA2/NAM7 helicase-like, C-terminal
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_006203-T1
|
-1.386200
|
IPR001841 Zinc finger, RING-type, IPR002867 IBR domain, IPR013083 Zinc finger, RING/FYVE/PHD-type, IPR017907 Zinc finger, RING-type, conserved site
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001955-T1
|
-1.387192
|
IPR001138 Zn(2)Cys(6) fungal-type DNA-binding domain, IPR001451 Hexapeptide repeat, IPR002110 Ankyrin repeat, IPR011004 Trimeric LpxA-like superfamily, IPR018357 Hexapeptide transferase, conserved site, IPR020683 Domain of unknown function DUF3447, IPR024688 Maltose/galactoside acetyltransferase, IPR036770 Ankyrin repeat-containing domain superfamily, IPR036864 Zn(2)-C6 fungal-type DNA-binding domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009761-T1
|
-1.387848
|
IPR001283 Cysteine-rich secretory protein-related, IPR014044 CAP domain, IPR018244 Allergen V5/Tpx-1-related, conserved site, IPR034120 None, IPR035940 CAP superfamily
|
NA
|
NA
|
K20412
|
TRUE
|
FALSE
|
|
XANPAGTX0501_002410-T1
|
-1.391729
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006114-T1
|
-1.393540
|
IPR001680 WD40 repeat, IPR015943 WD40/YVTN repeat-like-containing domain superfamily, IPR036322 WD40-repeat-containing domain superfamily
|
NA
|
NA
|
K12782
|
FALSE
|
FALSE
|
|
XANPAGTX0501_007365-T1
|
-1.397815
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009326-T1
|
-1.398307
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005584-T1
|
-1.398387
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001825-T1
|
-1.402807
|
IPR003663 Sugar/inositol transporter, IPR005828 Major facilitator, sugar transporter-like, IPR005829 Sugar transporter, conserved site, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_010380-T1
|
-1.404538
|
IPR000210 BTB/POZ domain, IPR011333 SKP1/BTB/POZ domain superfamily
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_000033-T1
|
-1.410231
|
IPR002656 Acyltransferase 3 domain
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009293-T1
|
-1.419596
|
NA
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_004008-T1
|
-1.420375
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000036-T1
|
-1.420457
|
IPR006640 SprT-like
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009581-T1
|
-1.427218
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008888-T1
|
-1.427796
|
IPR007527 Zinc finger, SWIM-type
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_003765-T1
|
-1.428029
|
IPR000420 Yeast PIR protein repeat
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_000697-T1
|
-1.443805
|
NA
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_006214-T1
|
-1.444244
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_009795-T2
|
-1.444535
|
IPR023631 Amidase signature domain, IPR036928 Amidase signature (AS) superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_010304-T1
|
-1.458420
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006422-T1
|
-1.460727
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004978-T1
|
-1.460984
|
NA
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_009621-T1
|
-1.461288
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006909-T1
|
-1.464054
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008863-T1
|
-1.466559
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002007-T1
|
-1.467093
|
NA
|
NA
|
NA
|
|
TRUE
|
TRUE
|
|
XANPAGTX0501_002820-T1
|
-1.467192
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_006246-T1
|
-1.468497
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_007869-T1
|
-1.472330
|
IPR000210 BTB/POZ domain, IPR011333 SKP1/BTB/POZ domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005619-T1
|
-1.474796
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_010379-T1
|
-1.475645
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008874-T1
|
-1.479109
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_006459-T1
|
-1.480266
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009605-T1
|
-1.480669
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002963-T1
|
-1.487093
|
IPR000172 Glucose-methanol-choline oxidoreductase, N-terminal, IPR007867 Glucose-methanol-choline oxidoreductase, C-terminal, IPR012132 Glucose-methanol-choline oxidoreductase, IPR036188 FAD/NAD(P)-binding domain superfamily
|
AA3
|
NA
|
K00108
|
TRUE
|
FALSE
|
|
XANPAGTX0501_009942-T1
|
-1.494661
|
IPR001810 F-box domain, IPR036047 F-box-like domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001951-T1
|
-1.498238
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004853-T1
|
-1.500419
|
IPR000719 Protein kinase domain, IPR000961 AGC-kinase, C-terminal, IPR011009 Protein kinase-like domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_003361-T1
|
-1.505428
|
NA
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_001820-T2
|
-1.510192
|
IPR021109 Aspartic peptidase domain superfamily, IPR033121 Peptidase family A1 domain
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000691-T1
|
-1.511934
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_001710-T1
|
-1.512838
|
IPR007577 Glycosyltransferase, DXD sugar-binding motif, IPR029044 Nucleotide-diphospho-sugar transferases
|
GT32
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_003448-T1
|
-1.515924
|
NA
|
NA
|
NA
|
|
TRUE
|
TRUE
|
|
XANPAGTX0501_000420-T1
|
-1.518444
|
IPR013087 Zinc finger C2H2-type
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005278-T1
|
-1.521181
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_010051-T1
|
-1.529828
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000910-T1
|
-1.530331
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009511-T1
|
-1.533303
|
IPR000757 Glycoside hydrolase family 16, IPR001002 Chitin-binding, type 1, IPR008264 Beta-glucanase, IPR013320 Concanavalin A-like lectin/glucanase domain superfamily, IPR036861 Endochitinase-like superfamily
|
GH16
|
NA
|
K01216
|
TRUE
|
FALSE
|
|
XANPAGTX0501_008533-T1
|
-1.540302
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009737-T1
|
-1.540774
|
IPR005829 Sugar transporter, conserved site, IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009141-T1
|
-1.543886
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_007899-T1
|
-1.544599
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_003247-T1
|
-1.545289
|
IPR001878 Zinc finger, CCHC-type, IPR025836 Zinc knuckle CX2CX4HX4C, IPR036875 Zinc finger, CCHC-type superfamily
|
NA
|
NA
|
K09250
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009666-T1
|
-1.554891
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001082-T1
|
-1.559541
|
IPR004853 Sugar phosphate transporter domain
|
NA
|
NA
|
K26222
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005402-T1
|
-1.560177
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_000872-T1
|
-1.562878
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005296-T1
|
-1.568716
|
IPR018750 Protein of unknown function DUF2306, membrane
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004018-T2
|
-1.571979
|
IPR011009 Protein kinase-like domain superfamily, IPR016477 Fructosamine/Ketosamine-3-kinase
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_007750-T1
|
-1.577297
|
IPR027417 P-loop containing nucleoside triphosphate hydrolase
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004416-T1
|
-1.578773
|
IPR000246 Peptidase T2, asparaginase 2, IPR029055 Nucleophile aminohydrolases, N-terminal, IPR037464 Threonine aspartase 1
|
NA
|
T02
|
K08657
|
FALSE
|
FALSE
|
|
XANPAGTX0501_007403-T1
|
-1.582309
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_010598-T1
|
-1.582325
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009600-T1
|
-1.583776
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_007231-T1
|
-1.583790
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_010381-T1
|
-1.592206
|
IPR002293 Amino acid/polyamine transporter I
|
NA
|
NA
|
K03294
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008534-T1
|
-1.593016
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001512-T1
|
-1.603338
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001061-T1
|
-1.603339
|
IPR002328 Alcohol dehydrogenase, zinc-type, conserved site, IPR011032 GroES-like superfamily, IPR013149 Alcohol dehydrogenase-like, C-terminal, IPR013154 Alcohol dehydrogenase-like, N-terminal, IPR020843 Polyketide synthase, enoylreductase domain, IPR036291 NAD(P)-binding domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001953-T1
|
-1.607205
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005049-T1
|
-1.612235
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002057-T1
|
-1.616294
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008008-T1
|
-1.617050
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006330-T1
|
-1.618394
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001064-T1
|
-1.621988
|
IPR021765 Mycotoxin biosynthesis protein UstYa-like
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009887-T1
|
-1.625740
|
NA
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_001965-T1
|
-1.632952
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008628-T1
|
-1.639869
|
IPR023346 Lysozyme-like domain superfamily
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_000025-T1
|
-1.641669
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_001362-T1
|
-1.647839
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_003283-T1
|
-1.648782
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001948-T1
|
-1.662753
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001888-T1
|
-1.678493
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001950-T1
|
-1.678963
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_007464-T1
|
-1.685849
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002213-T1
|
-1.688746
|
IPR000629 ATP-dependent RNA helicase DEAD-box, conserved site, IPR001650 Helicase, C-terminal, IPR011545 DEAD/DEAH box helicase domain, IPR014001 Helicase superfamily 1/2, ATP-binding domain, IPR014014 RNA helicase, DEAD-box type, Q motif, IPR027417 P-loop containing nucleoside triphosphate hydrolase
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009316-T1
|
-1.697722
|
IPR001810 F-box domain, IPR036047 F-box-like domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009886-T1
|
-1.705744
|
NA
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_003282-T1
|
-1.706541
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008426-T1
|
-1.707030
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001330-T1
|
-1.707882
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_000681-T1
|
-1.709567
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001964-T1
|
-1.727590
|
IPR001611 Leucine-rich repeat, IPR003591 Leucine-rich repeat, typical subtype, IPR019487 RAM signalling pathway, SOG2, IPR032675 Leucine-rich repeat domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001949-T1
|
-1.732732
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006245-T1
|
-1.743213
|
NA
|
NA
|
NA
|
|
TRUE
|
TRUE
|
|
XANPAGTX0501_003212-T1
|
-1.757104
|
IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily, IPR036047 F-box-like domain superfamily
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_009317-T1
|
-1.758003
|
IPR008979 Galactose-binding-like domain superfamily
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_009582-T1
|
-1.765103
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004217-T1
|
-1.766312
|
IPR000504 RNA recognition motif domain, IPR012677 Nucleotide-binding alpha-beta plait domain superfamily, IPR035979 RNA-binding domain superfamily
|
NA
|
NA
|
K24990
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005394-T1
|
-1.767362
|
IPR002575 Aminoglycoside phosphotransferase, IPR011009 Protein kinase-like domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001947-T1
|
-1.767840
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_003775-T1
|
-1.770114
|
IPR003100 PAZ domain, IPR003165 Piwi domain, IPR012337 Ribonuclease H-like superfamily, IPR014811 Argonaute, linker 1 domain, IPR032472 Argonaute linker 2 domain, IPR032473 Protein argonaute, Mid domain, IPR032474 Protein argonaute, N-terminal, IPR036085 PAZ domain superfamily, IPR036397 Ribonuclease H superfamily
|
NA
|
NA
|
K11593
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008419-T1
|
-1.778819
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004950-T1
|
-1.782824
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002170-T1
|
-1.786506
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000893-T1
|
-1.791529
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004628-T1
|
-1.792127
|
IPR002156 Ribonuclease H domain, IPR012337 Ribonuclease H-like superfamily, IPR036397 Ribonuclease H superfamily
|
NA
|
NA
|
K03469
|
FALSE
|
FALSE
|
|
XANPAGTX0501_007343-T1
|
-1.792140
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004494-T1
|
-1.792536
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_010117-T1
|
-1.793767
|
IPR002110 Ankyrin repeat, IPR011009 Protein kinase-like domain superfamily, IPR016477 Fructosamine/Ketosamine-3-kinase, IPR020683 Domain of unknown function DUF3447, IPR036770 Ankyrin repeat-containing domain superfamily
|
NA
|
NA
|
K15523
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006449-T1
|
-1.796457
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000005-T1
|
-1.801160
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005658-T1
|
-1.801278
|
IPR001153 Barwin domain, IPR009009 RlpA-like protein, double-psi beta-barrel domain, IPR036908 RlpA-like domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_003213-T1
|
-1.804291
|
IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily, IPR036047 F-box-like domain superfamily
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_001954-T1
|
-1.808672
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004580-T1
|
-1.809609
|
IPR007292 Nuclear fusion protein Kar5
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002103-T1
|
-1.810531
|
IPR036910 High mobility group box domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005597-T1
|
-1.816345
|
IPR006421 Glycogen debranching enzyme, metazoa, IPR008928 Six-hairpin glycosidase superfamily, IPR012341 Six-hairpin glycosidase-like superfamily, IPR017853 Glycoside hydrolase superfamily, IPR029436 Eukaryotic glycogen debranching enzyme, N-terminal domain, IPR032788 Glycogen debranching enzyme, central domain, IPR032790 Glycogen debranching enzyme, C-terminal, IPR032792 Glycogen debranching enzyme, glucanotransferase domain
|
GH133
|
NA
|
K01196
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005613-T1
|
-1.817996
|
IPR003615 HNH nuclease
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_006016-T1
|
-1.831989
|
IPR008928 Six-hairpin glycosidase superfamily, IPR031335 Glycosyl hydrolase family 63, C-terminal
|
GH63
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002104-T1
|
-1.835003
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_007067-T1
|
-1.839308
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_001612-T1
|
-1.846971
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000398-T1
|
-1.847702
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004493-T1
|
-1.857771
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_007244-T1
|
-1.858539
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000610-T1
|
-1.868687
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001333-T1
|
-1.870374
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_009927-T1
|
-1.870484
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_007870-T1
|
-1.874070
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004104-T1
|
-1.878122
|
IPR001214 SET domain, IPR011990 Tetratricopeptide-like helical domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005631-T1
|
-1.885566
|
IPR023631 Amidase signature domain, IPR036928 Amidase signature (AS) superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009786-T1
|
-1.894942
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002185-T1
|
-1.897085
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002163-T1
|
-1.904022
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006255-T1
|
-1.904541
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001643-T1
|
-1.910689
|
IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily, IPR036047 F-box-like domain superfamily
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_010222-T1
|
-1.912114
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002166-T1
|
-1.917720
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009926-T1
|
-1.919959
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000194-T1
|
-1.934433
|
IPR006047 Glycosyl hydrolase, family 13, catalytic domain, IPR013780 Glycosyl hydrolase, all-beta, IPR017853 Glycoside hydrolase superfamily
|
GH13
|
NA
|
K01176
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000647-T1
|
-1.940161
|
IPR000571 Zinc finger, CCCH-type
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001956-T1
|
-1.941094
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008090-T1
|
-1.954350
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002165-T1
|
-1.959472
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005620-T1
|
-1.973360
|
IPR001841 Zinc finger, RING-type, IPR004331 SPX domain, IPR011016 Zinc finger, RING-CH-type, IPR013083 Zinc finger, RING/FYVE/PHD-type, IPR017907 Zinc finger, RING-type, conserved site
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_004520-T1
|
-1.985803
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001605-T1
|
-1.990522
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001538-T1
|
-1.994056
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001414-T1
|
-1.994528
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005048-T1
|
-1.997677
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000604-T1
|
-1.997943
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001958-T1
|
-1.998637
|
IPR001356 Homeobox domain, IPR009057 Homeobox-like domain superfamily, IPR017970 Homeobox, conserved site
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006974-T1
|
-2.000740
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009615-T1
|
-2.000853
|
IPR035940 CAP superfamily
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_001952-T1
|
-2.002699
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008041-T1
|
-2.016189
|
NA
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_005630-T1
|
-2.027229
|
IPR036928 Amidase signature (AS) superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002522-T1
|
-2.030035
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006910-T1
|
-2.032529
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001967-T1
|
-2.032808
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_003572-T1
|
-2.044217
|
IPR001087 GDSL lipase/esterase, IPR036514 SGNH hydrolase superfamily
|
CE16
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_010303-T1
|
-2.054768
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005279-T1
|
-2.055973
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009139-T1
|
-2.056685
|
IPR001876 Zinc finger, RanBP2-type
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004891-T1
|
-2.057500
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001910-T1
|
-2.062241
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_007873-T1
|
-2.067522
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_007871-T1
|
-2.081123
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_005615-T1
|
-2.092197
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009318-T1
|
-2.097684
|
IPR011333 SKP1/BTB/POZ domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005735-T1
|
-2.102015
|
IPR018824 Conidiation-specific protein 6
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_007872-T1
|
-2.105800
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_001611-T1
|
-2.125697
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005814-T1
|
-2.129685
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001859-T1
|
-2.142380
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_007262-T1
|
-2.149005
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_010203-T1
|
-2.149005
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_008856-T1
|
-2.160218
|
IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_005061-T1
|
-2.166875
|
NA
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_002183-T1
|
-2.174606
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002182-T1
|
-2.180402
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002763-T1
|
-2.184556
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009619-T1
|
-2.203533
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005766-T1
|
-2.223453
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004414-T1
|
-2.230880
|
IPR027417 P-loop containing nucleoside triphosphate hydrolase
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_006957-T1
|
-2.252415
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005614-T1
|
-2.252890
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001960-T1
|
-2.264721
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_010596-T1
|
-2.271872
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000193-T1
|
-2.283992
|
IPR006047 Glycosyl hydrolase, family 13, catalytic domain, IPR017853 Glycoside hydrolase superfamily
|
GH13
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004521-T1
|
-2.284391
|
IPR008271 Serine/threonine-protein kinase, active site, IPR011009 Protein kinase-like domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002172-T1
|
-2.285092
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008331-T1
|
-2.302060
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002184-T1
|
-2.304675
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004966-T1
|
-2.317059
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001959-T1
|
-2.362237
|
IPR000095 CRIB domain, IPR000719 Protein kinase domain, IPR008271 Serine/threonine-protein kinase, active site, IPR011009 Protein kinase-like domain superfamily, IPR017441 Protein kinase, ATP binding site, IPR033923 p21 activated kinase binding domain, IPR036936 CRIB domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001063-T1
|
-2.369606
|
NA
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_008284-T1
|
-2.429045
|
IPR029044 Nucleotide-diphospho-sugar transferases
|
GT2_Glyco_tranf_2
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008782-T1
|
-2.431407
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001966-T1
|
-2.436706
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_003209-T1
|
-2.437600
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008009-T1
|
-2.444813
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001962-T1
|
-2.456164
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008007-T1
|
-2.479715
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_007397-T1
|
-2.486783
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000378-T1
|
-2.490902
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009602-T1
|
-2.500879
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006951-T1
|
-2.507920
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002164-T1
|
-2.527734
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001856-T1
|
-2.592477
|
IPR037176 Osmotin/thaumatin-like superfamily
|
NA
|
NA
|
|
TRUE
|
TRUE
|
|
XANPAGTX0501_007900-T1
|
-2.636563
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_006327-T1
|
-2.649849
|
IPR018466 Yeast cell wall synthesis Kre9/Knh1-like, N-terminal
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_002506-T1
|
-2.726475
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_010050-T2
|
-2.757580
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_003211-T1
|
-2.931999
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_007239-T1
|
-3.420906
|
IPR027417 P-loop containing nucleoside triphosphate hydrolase
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008519-T2
|
-4.617470
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
- Selected only genes that are potentially multicellularity related
mult_gene_table_ap2<-mult_gene_table %>% inner_join(ea_sig %>% filter(change=="apothecium") %>% select(target_id,b),by=c("TranscriptID"="target_id")) %>% arrange(Function)
mult_gene_table_ap2 %>%
kable(format = "html", col.names = colnames(mult_gene_table_ap2)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
|
TranscriptID
|
ID
|
Annotation_type
|
Description
|
Function
|
Function_type
|
b
|
|
XANPAGTX0501_001061-T1
|
IPR013149
|
IPR
|
Alcohol dehydrogenase-like, C-terminal
|
Acetyl-CoA production and metabolism
|
Fungal multicellularity
|
-1.603339
|
|
XANPAGTX0501_005597-T1
|
IPR032788
|
IPR
|
Glycogen debranching enzyme, central domain
|
Carbohydrate storage
|
Fungal multicellularity
|
-1.816345
|
|
XANPAGTX0501_000647-T1
|
IPR000571
|
IPR
|
Zinc finger, CCCH-type
|
Cell division, proliferation and growth
|
Fungal multicellularity
|
-1.940161
|
|
XANPAGTX0501_002213-T1
|
IPR001650
|
IPR
|
Helicase, C-terminal
|
Cell division, proliferation and growth
|
Fungal multicellularity
|
-1.688746
|
|
XANPAGTX0501_003775-T1
|
IPR012337
|
IPR
|
Ribonuclease H-like superfamily
|
Cell division, proliferation and growth
|
Fungal multicellularity
|
-1.770114
|
|
XANPAGTX0501_003775-T2
|
IPR012337
|
IPR
|
Ribonuclease H-like superfamily
|
Cell division, proliferation and growth
|
Fungal multicellularity
|
-1.260916
|
|
XANPAGTX0501_004104-T1
|
IPR001214
|
IPR
|
SET domain
|
Cell division, proliferation and growth
|
Fungal multicellularity
|
-1.878122
|
|
XANPAGTX0501_004244-T1
|
IPR012337
|
IPR
|
Ribonuclease H-like superfamily
|
Cell division, proliferation and growth
|
Fungal multicellularity
|
-1.139706
|
|
XANPAGTX0501_004628-T1
|
IPR012337
|
IPR
|
Ribonuclease H-like superfamily
|
Cell division, proliferation and growth
|
Fungal multicellularity
|
-1.792127
|
|
XANPAGTX0501_003124-T1
|
IPR001461
|
IPR
|
Aspartic peptidase A1 family
|
Cell surface and cell wall proteins
|
Fungal multicellularity
|
-1.348872
|
|
XANPAGTX0501_005735-T1
|
IPR018824
|
IPR
|
Conidiation-specific protein 6
|
Cell surface and cell wall proteins
|
Fungal multicellularity
|
-2.102015
|
|
XANPAGTX0501_006327-T1
|
IPR018466
|
IPR
|
Yeast cell wall synthesis Kre9/Knh1-like, N-terminal
|
Cell wall biosynthesis
|
Fungal multicellularity
|
-2.649849
|
|
XANPAGTX0501_000203-T1
|
IPR037176
|
IPR
|
Osmotin/thaumatin-like superfamily
|
Cell wall remodeling
|
Fungal multicellularity
|
-1.040557
|
|
XANPAGTX0501_001856-T1
|
IPR037176
|
IPR
|
Osmotin/thaumatin-like superfamily
|
Cell wall remodeling
|
Fungal multicellularity
|
-2.592477
|
|
XANPAGTX0501_007833-T1
|
IPR002889
|
IPR
|
Carbohydrate-binding WSC
|
Cell wall remodeling
|
Fungal multicellularity
|
-1.343993
|
|
XANPAGTX0501_009511-T1
|
GH16
|
CAZy
|
act on beta-1,4 or beta-1,3 glycosidic bonds in glucans and galactans
|
Cell wall remodeling
|
Fungal multicellularity
|
-1.533303
|
|
XANPAGTX0501_006767-T1
|
IPR017956
|
IPR
|
AT hook, DNA-binding motif
|
Chromatin regulation
|
Expression regulation
|
-1.001121
|
|
XANPAGTX0501_001064-T1
|
IPR021765
|
IPR
|
Mycotoxin biosynthesis protein UstYa-like
|
Defense
|
Fungal multicellularity
|
-1.621988
|
|
XANPAGTX0501_001643-T1
|
IPR001810
|
IPR
|
F-box domain
|
Protein ubiquitination
|
Fungal multicellularity
|
-1.910689
|
|
XANPAGTX0501_003212-T1
|
IPR001810
|
IPR
|
F-box domain
|
Protein ubiquitination
|
Fungal multicellularity
|
-1.757104
|
|
XANPAGTX0501_003213-T1
|
IPR001810
|
IPR
|
F-box domain
|
Protein ubiquitination
|
Fungal multicellularity
|
-1.804291
|
|
XANPAGTX0501_003264-T1
|
IPR000210
|
IPR
|
BTB/POZ domain
|
Protein ubiquitination
|
Fungal multicellularity
|
-1.264968
|
|
XANPAGTX0501_005550-T1
|
IPR001810
|
IPR
|
F-box domain
|
Protein ubiquitination
|
Fungal multicellularity
|
-1.294683
|
|
XANPAGTX0501_005620-T1
|
IPR017907
|
IPR
|
Zinc finger; RING-type; conserved site
|
Protein ubiquitination
|
Fungal multicellularity
|
-1.973360
|
|
XANPAGTX0501_006203-T1
|
IPR017907
|
IPR
|
Zinc finger; RING-type; conserved site
|
Protein ubiquitination
|
Fungal multicellularity
|
-1.386200
|
|
XANPAGTX0501_007869-T1
|
IPR000210
|
IPR
|
BTB/POZ domain
|
Protein ubiquitination
|
Fungal multicellularity
|
-1.472330
|
|
XANPAGTX0501_008856-T1
|
IPR001810
|
IPR
|
F-box domain
|
Protein ubiquitination
|
Fungal multicellularity
|
-2.160218
|
|
XANPAGTX0501_009316-T1
|
IPR001810
|
IPR
|
F-box domain
|
Protein ubiquitination
|
Fungal multicellularity
|
-1.697722
|
|
XANPAGTX0501_009738-T1
|
IPR001810
|
IPR
|
F-box domain
|
Protein ubiquitination
|
Fungal multicellularity
|
-1.170585
|
|
XANPAGTX0501_009942-T1
|
IPR001810
|
IPR
|
F-box domain
|
Protein ubiquitination
|
Fungal multicellularity
|
-1.494661
|
|
XANPAGTX0501_010380-T1
|
IPR000210
|
IPR
|
BTB/POZ domain
|
Protein ubiquitination
|
Fungal multicellularity
|
-1.404538
|
|
XANPAGTX0501_001648-T1
|
IPR000504
|
IPR
|
RNA recognition motif domain
|
RNA binding proteins
|
Expression regulation
|
-1.214948
|
|
XANPAGTX0501_002098-T1
|
IPR000504
|
IPR
|
RNA recognition motif domain
|
RNA binding proteins
|
Expression regulation
|
-1.334348
|
|
XANPAGTX0501_002123-T1
|
IPR000504
|
IPR
|
RNA recognition motif domain
|
RNA binding proteins
|
Expression regulation
|
-1.312729
|
|
XANPAGTX0501_004217-T1
|
IPR000504
|
IPR
|
RNA recognition motif domain
|
RNA binding proteins
|
Expression regulation
|
-1.766312
|
|
XANPAGTX0501_005177-T1
|
IPR001313
|
IPR
|
Pumilio RNA-binding repeat
|
RNA binding proteins
|
Expression regulation
|
-1.185673
|
|
XANPAGTX0501_002123-T1
|
IPR007855
|
IPR
|
RNA-dependent RNA polymerase, eukaryotic-type
|
RNA interference
|
Expression regulation
|
-1.312729
|
|
XANPAGTX0501_003775-T1
|
IPR032474
|
IPR
|
Protein argonaute, N-terminal
|
RNA interference
|
Expression regulation
|
-1.770114
|
|
XANPAGTX0501_003775-T2
|
IPR032474
|
IPR
|
Protein argonaute, N-terminal
|
RNA interference
|
Expression regulation
|
-1.260916
|
|
XANPAGTX0501_004244-T1
|
IPR032474
|
IPR
|
Protein argonaute, N-terminal
|
RNA interference
|
Expression regulation
|
-1.139706
|
|
XANPAGTX0501_000420-T1
|
IPR013087
|
IPR
|
Zinc finger C2H2-type
|
Transcription factors
|
Expression regulation
|
-1.518444
|
|
XANPAGTX0501_001955-T1
|
IPR036864
|
IPR
|
Zn(2)-C6 fungal-type DNA-binding domain superfamily
|
Transcription factors
|
Expression regulation
|
-1.387192
|
|
XANPAGTX0501_001958-T1
|
IPR001356
|
IPR
|
Homeobox domain
|
Transcription factors
|
Expression regulation
|
-1.998637
|
|
XANPAGTX0501_005620-T1
|
IPR013083
|
IPR
|
Zinc finger, RING/FYVE/PHD-type
|
Transcription factors
|
Expression regulation
|
-1.973360
|
|
XANPAGTX0501_005640-T1
|
IPR013087
|
IPR
|
Zinc finger C2H2-type
|
Transcription factors
|
Expression regulation
|
-1.380432
|
|
XANPAGTX0501_006203-T1
|
IPR013083
|
IPR
|
Zinc finger, RING/FYVE/PHD-type
|
Transcription factors
|
Expression regulation
|
-1.386200
|
|
XANPAGTX0501_006931-T1
|
IPR013087
|
IPR
|
Zinc finger C2H2-type
|
Transcription factors
|
Expression regulation
|
-1.072494
|
|
XANPAGTX0501_008005-T1
|
IPR013083
|
IPR
|
Zinc finger, RING/FYVE/PHD-type
|
Transcription factors
|
Expression regulation
|
-1.251448
|
|
XANPAGTX0501_000281-T1
|
IPR036259
|
IPR
|
MFS transporter superfamily
|
Transporters
|
Fungal multicellularity
|
-1.282182
|
|
XANPAGTX0501_001825-T1
|
IPR036259
|
IPR
|
MFS transporter superfamily
|
Transporters
|
Fungal multicellularity
|
-1.402807
|
|
XANPAGTX0501_008594-T1
|
IPR036259
|
IPR
|
MFS transporter superfamily
|
Transporters
|
Fungal multicellularity
|
-1.040188
|
|
XANPAGTX0501_009737-T1
|
IPR036259
|
IPR
|
MFS transporter superfamily
|
Transporters
|
Fungal multicellularity
|
-1.540774
|
Notably, many TFs and ubiquitin degradation proteins
Also many transporters, which wasn’t the case in other lists here
Enrichment analysis
enrich2<-clusterProfiler::enricher(ap_ea_genes$target_id,
pAdjustMethod = "none",
minGSSize = 1,
maxGSSize = 2000,
qvalueCutoff = 1,
universe=ips_data$universe,
TERM2GENE=ips_data$term2protein,
TERM2NAME=ips_data$term2name)
enrich_pairwise2<-enrichplot::pairwise_termsim(enrich2)
enrichplot::emapplot(enrich_pairwise2)

Upregulated in edge
- Bootstrap of the two genes most overexpressed in the edge
plot_bootstrap(ea_so,
target_id = ea_sig$target_id[which.max(ea_sig$b)],
units = "est_counts",
color_by = "part")
plot_bootstrap(ea_so,
target_id = ea_sig$target_id[which.max(ea_sig$b[-which.max(ea_sig$b)])],
units = "est_counts",
color_by = "part")


- Of the 13 upregulated in edge, 3 have no functional annotations
- 6 are secreted
ed_ea_genes<-ea_sig %>% filter(change=="edge") %>%
left_join(funannot2,by=c("target_id"="TranscriptID")) %>%
select(target_id,b,InterPro_new,CAZyme_new,Protease_new,KO,secreted_consensus,lichen_ortho)
ed_ea_genes %>%
kable(format = "html", col.names = colnames(ap_ea_genes)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
|
target_id
|
b
|
InterPro_new
|
CAZyme_new
|
Protease_new
|
KO
|
secreted_consensus
|
lichen_ortho
|
|
XANPAGTX0501_010431-T1
|
1.523359
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001015-T1
|
1.339807
|
IPR001153 Barwin domain, IPR009009 RlpA-like protein, double-psi beta-barrel domain, IPR036908 RlpA-like domain superfamily
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_006189-T1
|
1.275509
|
IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002706-T1
|
1.129817
|
IPR002129 Pyridoxal phosphate-dependent decarboxylase, IPR015421 Pyridoxal phosphate-dependent transferase, major domain, IPR015424 Pyridoxal phosphate-dependent transferase
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004034-T1
|
1.121819
|
NA
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_010624-T1
|
1.121535
|
IPR023631 Amidase signature domain, IPR036928 Amidase signature (AS) superfamily
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_004943-T2
|
1.117316
|
IPR002020 Citrate synthase, IPR016142 Citrate synthase-like, large alpha subdomain, IPR016143 Citrate synthase-like, small alpha subdomain, IPR019810 Citrate synthase active site, IPR036969 Citrate synthase superfamily
|
NA
|
NA
|
K01647
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006869-T1
|
1.099929
|
IPR008979 Galactose-binding-like domain superfamily, IPR017853 Glycoside hydrolase superfamily, IPR024655 Asl1-like, glycosyl hydrolase catalytic domain
|
GH128
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_004633-T1
|
1.094695
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_010430-T1
|
1.093667
|
IPR000542 Acyltransferase ChoActase/COT/CPT, IPR001227 Acyl transferase domain superfamily, IPR006162 Phosphopantetheine attachment site, IPR009081 Phosphopantetheine binding ACP domain, IPR011032 GroES-like superfamily, IPR013217 Methyltransferase type 12, IPR013968 Polyketide synthase, ketoreductase domain, IPR014030 Beta-ketoacyl synthase, N-terminal, IPR014031 Beta-ketoacyl synthase, C-terminal, IPR014043 Acyl transferase, IPR016035 Acyl transferase/acyl hydrolase/lysophospholipase, IPR016036 Malonyl-CoA ACP transacylase, ACP-binding, IPR016039 Thiolase-like, IPR020801 None, IPR020806 Polyketide synthase, phosphopantetheine-binding domain, IPR020807 Polyketide synthase, dehydratase domain, IPR020841 Polyketide synthase, beta-ketoacyl synthase domain, IPR020843 Polyketide synthase, enoylreductase domain, IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily, IPR032821 Polyketide synthase, C-terminal extension, IPR036291 NAD(P)-binding domain superfamily, IPR036736 ACP-like superfamily, IPR039551 Choline/carnitine acyltransferase domain, IPR042104 Polyketide synthase, dehydratase domain superfamily, IPR042231 Choline/Carnitine o-acyltransferase, domain 2, IPR042232 None
|
NA
|
NA
|
K12443
|
FALSE
|
TRUE
|
|
XANPAGTX0501_001458-T1
|
1.026449
|
IPR002889 Carbohydrate-binding WSC, IPR018535 Domain of unknown function DUF1996
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_009181-T1
|
1.024662
|
IPR008427 Extracellular membrane protein, CFEM domain
|
NA
|
NA
|
|
TRUE
|
TRUE
|
|
XANPAGTX0501_008853-T1
|
1.003145
|
IPR009799 EthD domain, IPR011008 Dimeric alpha-beta barrel
|
NA
|
NA
|
|
FALSE
|
FALSE
|
Parietin cluster is upregulated in the edge
- One of the proteins in the parietin BGC, an extra one
plot_bootstrap(ea_so,
target_id = "XANPAGTX0501_008853-T1",
units = "est_counts",
color_by = "part")

- The main PKS gene is just below the threshold (b = 0.92)
plot_bootstrap(ea_so,
target_id = "XANPAGTX0501_008852-T1",
units = "est_counts",
color_by = "part")

4.2. Power analysis: simple
- Do we have enough samples for this comparison?
- Looked at the distribution of corrected p-values (a.k.a. q-values). The graph looks good: close to uniform, with an increase close to 0. If our test was underpowered, we would see an increase of p-vlaues along 0->1, but this is not the case
ggplot(ea_table)+geom_histogram(aes(x=qval))
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
## Warning: Removed 690798 rows containing non-finite values (`stat_bin()`).

library(MKpower)
qqunif(ea_table$qval, color.line = "orange")

5. How similar are gene lists between comparisons?
Upregulated in the edge
- Only one gene upregulated compared to the center, and it is also in the second list
library(ggVennDiagram)
##
## Attaching package: 'ggVennDiagram'
## The following object is masked from 'package:tidyr':
##
## unite
venn_e<-list(compared_to_apothecia = ea_sig$target_id[ea_sig$change=="edge"],
compared_to_center = ec_sig$target_id[ec_sig$b>0.9])
e<-ggVennDiagram(venn_e,label_size = 5,set_size=5)+labs(title = "Upregulated in edge")+theme(title=element_text(size=12))+scale_x_continuous(expand = expansion(mult = .4))
e

Upregulated in the center
- Compared to apothecia one is upregulated, and it’s not in the second list
venn_c<-list(compared_to_apothecia = ca_sig$target_id[ca_sig$change=="centre"],
compared_to_edge = ec_sig$target_id[ec_sig$change=="centre"])
c<-ggVennDiagram(venn_c,label_size = 5,set_size=5)+labs(title = "Upregulated in center")+theme(title=element_text(size=12))+scale_x_continuous(expand = expansion(mult = .4))
c

Upregulated in the apothecia
- These lists are large, and the smaller is almost entirely overlapping with the bigger one
venn_a<-list(compared_to_center = ca_sig$target_id[ca_sig$change=="apothecium"],
compared_to_edge = ea_sig$target_id[ea_sig$change=="apothecium"])
a<-ggVennDiagram(venn_a,label_size = 5,set_size=5)+labs(title = "Upregulated in apothecia")+theme(title=element_text(size=12))+scale_x_continuous(expand = expansion(mult = .4))
a

6. Comparing apothecia vs center+edge
Since there was so little difference between edge and center, pooled them together
250 upregulated in apothecia, only 2 in thallus
kal_dirs2 <-kal_dirs2 %>% mutate(part2 = ifelse(part =="apothecia","apothecia","thallus") )
kal_dirs2$part2 <- as.factor(kal_dirs2$part2)
kal_dirs2$thallus<- as.factor(kal_dirs2$thallus)
rhdf5::h5closeAll()
a_so <- sleuth_prep(kal_dirs2,extra_bootstrap_summary = TRUE,filter_target_id = target_id,transformation_function = function(x) log2(x + 0.1))
## Warning in check_num_cores(num_cores): It appears that you are running Sleuth from within Rstudio.
## Because of concerns with forking processes from a GUI, 'num_cores' is being set to 1.
## If you wish to take advantage of multiple cores, please consider running sleuth from the command line.
## reading in kallisto results
## dropping unused factor levels
## .................
## normalizing est_counts
## A list of target IDs for filtering was found. Using this for filtering
## 11083 targets passed the filter
## normalizing tpm
## merging in metadata
## summarizing bootstraps
## .................
#model that includes only confounding variables
a_so <- sleuth_fit(a_so, ~thallus, 'reduced')
## fitting measurement error models
## shrinkage estimation
## 1 NA values were found during variance shrinkage estimation due to mean observation values outside of the range used for the LOESS fit.
## The LOESS fit will be repeated using exact computation of the fitted surface to extrapolate the missing values.
## These are the target ids with NA values: XANPAGTX0501_000967-T1
## computing variance of betas
#model that includes only both the confounding variable and the variable of interest
a_so <- sleuth_fit(a_so, ~ thallus + part2, 'full')
## fitting measurement error models
## shrinkage estimation
## 4 NA values were found during variance shrinkage estimation due to mean observation values outside of the range used for the LOESS fit.
## The LOESS fit will be repeated using exact computation of the fitted surface to extrapolate the missing values.
## These are the target ids with NA values: XANPAGTX0501_000967-T1, XANPAGTX0501_001127-T1, XANPAGTX0501_002409-T1, XANPAGTX0501_010086-T1
## computing variance of betas
#compare the models
a_so <- sleuth_lrt(a_so, 'reduced', 'full')
a_so <- sleuth_wt(a_so, 'part2thallus')
a_table <- sleuth_results(a_so, 'part2thallus')
a_sig <- a_table %>% tibble::as_tibble() %>%
filter( qval <= 0.05, grepl("GTX0501",target_id) ) %>%
arrange(desc(b)) %>% mutate(change = if_else(b > 1, "thallus", ifelse(b< -1, "apothecium", "low_logFC")))
table(a_sig$change)
##
## apothecium low_logFC thallus
## 250 2746 2
library(RColorBrewer)
color_scheme<-c("apothecia"=brewer.pal(3,"Dark2")[1],
"thallus_centre"=brewer.pal(3,"Dark2")[2],
"thallus_edge" =brewer.pal(3,"Dark2")[3] )
plot_pca(a_so, color_by = 'part', text_labels = TRUE,use_filtered=T,units="tpm")+
theme_bw()+theme(text=element_text(size=7))+
scale_color_manual(values=color_scheme)

ggsave('../results/tissue_pca.pdf',width = 4.5, height = 3)
- Get % of variance explained
ppv <- plot_pc_variance(a_so,use_filtered=T,units="tpm")
PCpc <- ppv$data$var
names(PCpc) <- paste0("PC", seq(1:length(PCpc)))
PCpc
## PC1 PC2 PC3 PC4 PC5
## 59.109671 21.268849 11.537806 2.492545 1.805103
Upregulated in thallus
plot_bootstrap(a_so,
target_id = a_sig$target_id[which.max(a_sig$b)],
units = "est_counts",
color_by = "part2")
plot_bootstrap(a_so,
target_id = a_sig$target_id[which.max(a_sig$b[-which.max(a_sig$b)])],
units = "est_counts",
color_by = "part2")


- XANPAGTX0501_009376-T1 was not DGE in the edge/apothecia and center/apothecia comparisons
- XANPAGTX0501_004633-T1 was upregulated in the edge in the edge/apothecia, and nearly upregulated in center/apothecia (b value = 0.977)
- has no annotations, see above
a_genes<-a_sig %>% filter(b>0.9) %>%
left_join(funannot2,by=c("target_id"="TranscriptID")) %>%
select(target_id,b,InterPro_new,CAZyme_new,Protease_new,KO,secreted_consensus,lichen_ortho)
a_genes %>%
kable(format = "html", col.names = colnames(a_genes)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
|
target_id
|
b
|
InterPro_new
|
CAZyme_new
|
Protease_new
|
KO
|
secreted_consensus
|
lichen_ortho
|
|
XANPAGTX0501_009376-T1
|
2.4961545
|
IPR043141 Ribosomal protein L10-like domain superfamily
|
NA
|
NA
|
K02864
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004633-T1
|
1.0318823
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009913-T1
|
0.9922726
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_002706-T1
|
0.9523073
|
IPR002129 Pyridoxal phosphate-dependent decarboxylase, IPR015421 Pyridoxal phosphate-dependent transferase, major domain, IPR015424 Pyridoxal phosphate-dependent transferase
|
NA
|
NA
|
|
FALSE
|
FALSE
|
Upregulated in apothecia
- Of the 250 upregulated in apothecia, 171 have no functional annotations
- 24 are secreted
ap_a_genes<-a_sig %>% filter(change=="apothecium") %>%
left_join(funannot2,by=c("target_id"="TranscriptID")) %>%
select(target_id,b,InterPro_new,CAZyme_new,Protease_new,KO,secreted_consensus,lichen_ortho)
ap_a_genes %>%
kable(format = "html", col.names = colnames(ap_a_genes)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
|
target_id
|
b
|
InterPro_new
|
CAZyme_new
|
Protease_new
|
KO
|
secreted_consensus
|
lichen_ortho
|
|
XANPAGTX0501_007851-T1
|
-1.000996
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009787-T1
|
-1.001679
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000938-T1
|
-1.002687
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_007833-T1
|
-1.003237
|
IPR002889 Carbohydrate-binding WSC, IPR018535 Domain of unknown function DUF1996
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001498-T1
|
-1.006175
|
IPR012340 Nucleic acid-binding, OB-fold
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005188-T1
|
-1.006230
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_003775-T2
|
-1.015597
|
IPR003100 PAZ domain, IPR003165 Piwi domain, IPR012337 Ribonuclease H-like superfamily, IPR014811 Argonaute, linker 1 domain, IPR032472 Argonaute linker 2 domain, IPR032473 Protein argonaute, Mid domain, IPR032474 Protein argonaute, N-terminal, IPR036085 PAZ domain superfamily, IPR036397 Ribonuclease H superfamily
|
NA
|
NA
|
K11593
|
FALSE
|
FALSE
|
|
XANPAGTX0501_007473-T1
|
-1.021407
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_003790-T1
|
-1.024429
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_006420-T1
|
-1.025603
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001955-T1
|
-1.028447
|
IPR001138 Zn(2)Cys(6) fungal-type DNA-binding domain, IPR001451 Hexapeptide repeat, IPR002110 Ankyrin repeat, IPR011004 Trimeric LpxA-like superfamily, IPR018357 Hexapeptide transferase, conserved site, IPR020683 Domain of unknown function DUF3447, IPR024688 Maltose/galactoside acetyltransferase, IPR036770 Ankyrin repeat-containing domain superfamily, IPR036864 Zn(2)-C6 fungal-type DNA-binding domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_003033-T1
|
-1.030286
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002054-T1
|
-1.034049
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_003124-T1
|
-1.035285
|
IPR001461 Aspartic peptidase A1 family, IPR001969 Aspartic peptidase, active site, IPR021109 Aspartic peptidase domain superfamily, IPR033121 Peptidase family A1 domain, IPR034164 Pepsin-like domain
|
NA
|
A01A
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_002946-T1
|
-1.035401
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_002142-T1
|
-1.036917
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009581-T1
|
-1.037279
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004753-T1
|
-1.037567
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_003765-T1
|
-1.038156
|
IPR000420 Yeast PIR protein repeat
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_004978-T1
|
-1.047426
|
NA
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_004466-T1
|
-1.048483
|
IPR000490 Glycoside hydrolase family 17, IPR017853 Glycoside hydrolase superfamily, IPR018620 Ubiquitin 3 binding protein But2, C-terminal
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_006422-T1
|
-1.053965
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005317-T1
|
-1.054307
|
NA
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_006975-T1
|
-1.054818
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000622-T1
|
-1.055181
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002098-T1
|
-1.056175
|
IPR000504 RNA recognition motif domain, IPR012677 Nucleotide-binding alpha-beta plait domain superfamily, IPR035979 RNA-binding domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_007365-T1
|
-1.056362
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004102-T1
|
-1.058681
|
IPR000420 Yeast PIR protein repeat
|
NA
|
NA
|
K26550
|
TRUE
|
FALSE
|
|
XANPAGTX0501_001825-T1
|
-1.063406
|
IPR003663 Sugar/inositol transporter, IPR005828 Major facilitator, sugar transporter-like, IPR005829 Sugar transporter, conserved site, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001223-T1
|
-1.064214
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005815-T1
|
-1.064277
|
IPR000210 BTB/POZ domain, IPR011333 SKP1/BTB/POZ domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000036-T1
|
-1.068838
|
IPR006640 SprT-like
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002019-T1
|
-1.070414
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005619-T1
|
-1.070482
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009599-T1
|
-1.070929
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001964-T1
|
-1.071179
|
IPR001611 Leucine-rich repeat, IPR003591 Leucine-rich repeat, typical subtype, IPR019487 RAM signalling pathway, SOG2, IPR032675 Leucine-rich repeat domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000888-T1
|
-1.071659
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009795-T2
|
-1.071736
|
IPR023631 Amidase signature domain, IPR036928 Amidase signature (AS) superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008200-T1
|
-1.073076
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008888-T1
|
-1.075701
|
IPR007527 Zinc finger, SWIM-type
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_010001-T1
|
-1.075953
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_010379-T1
|
-1.076421
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001965-T1
|
-1.078800
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_010094-T1
|
-1.079269
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006459-T1
|
-1.089552
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002123-T1
|
-1.092697
|
IPR000504 RNA recognition motif domain, IPR007855 RNA-dependent RNA polymerase, eukaryotic-type, IPR035979 RNA-binding domain superfamily
|
NA
|
NA
|
K11699
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009326-T1
|
-1.097552
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001948-T1
|
-1.099351
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009293-T1
|
-1.101651
|
NA
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_007899-T1
|
-1.103335
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000420-T1
|
-1.104047
|
IPR013087 Zinc finger C2H2-type
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006246-T1
|
-1.104366
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006114-T1
|
-1.104804
|
IPR001680 WD40 repeat, IPR015943 WD40/YVTN repeat-like-containing domain superfamily, IPR036322 WD40-repeat-containing domain superfamily
|
NA
|
NA
|
K12782
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006310-T1
|
-1.105045
|
IPR022137 Zinc finger protein, DUF3669 domain
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001963-T1
|
-1.111833
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004008-T1
|
-1.117183
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002410-T1
|
-1.117363
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002963-T1
|
-1.118354
|
IPR000172 Glucose-methanol-choline oxidoreductase, N-terminal, IPR007867 Glucose-methanol-choline oxidoreductase, C-terminal, IPR012132 Glucose-methanol-choline oxidoreductase, IPR036188 FAD/NAD(P)-binding domain superfamily
|
AA3
|
NA
|
K00108
|
TRUE
|
FALSE
|
|
XANPAGTX0501_006909-T1
|
-1.120330
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_010145-T1
|
-1.120565
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_005584-T1
|
-1.124341
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002007-T1
|
-1.126910
|
NA
|
NA
|
NA
|
|
TRUE
|
TRUE
|
|
XANPAGTX0501_005278-T1
|
-1.128439
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000872-T1
|
-1.128589
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001710-T1
|
-1.130646
|
IPR007577 Glycosyltransferase, DXD sugar-binding motif, IPR029044 Nucleotide-diphospho-sugar transferases
|
GT32
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_007869-T1
|
-1.136332
|
IPR000210 BTB/POZ domain, IPR011333 SKP1/BTB/POZ domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009511-T1
|
-1.136478
|
IPR000757 Glycoside hydrolase family 16, IPR001002 Chitin-binding, type 1, IPR008264 Beta-glucanase, IPR013320 Concanavalin A-like lectin/glucanase domain superfamily, IPR036861 Endochitinase-like superfamily
|
GH16
|
NA
|
K01216
|
TRUE
|
FALSE
|
|
XANPAGTX0501_000691-T1
|
-1.140810
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_010007-T1
|
-1.146366
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001820-T2
|
-1.147375
|
IPR021109 Aspartic peptidase domain superfamily, IPR033121 Peptidase family A1 domain
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008863-T1
|
-1.149308
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_010381-T1
|
-1.157248
|
IPR002293 Amino acid/polyamine transporter I
|
NA
|
NA
|
K03294
|
FALSE
|
FALSE
|
|
XANPAGTX0501_003361-T1
|
-1.157393
|
NA
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_009666-T1
|
-1.163354
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000910-T1
|
-1.164861
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009942-T1
|
-1.164912
|
IPR001810 F-box domain, IPR036047 F-box-like domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008874-T1
|
-1.168644
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_005296-T1
|
-1.170842
|
IPR018750 Protein of unknown function DUF2306, membrane
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004853-T1
|
-1.170891
|
IPR000719 Protein kinase domain, IPR000961 AGC-kinase, C-terminal, IPR011009 Protein kinase-like domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001512-T1
|
-1.171326
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006203-T1
|
-1.175049
|
IPR001841 Zinc finger, RING-type, IPR002867 IBR domain, IPR013083 Zinc finger, RING/FYVE/PHD-type, IPR017907 Zinc finger, RING-type, conserved site
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001436-T1
|
-1.178216
|
IPR002048 EF-hand domain, IPR011992 EF-hand domain pair, IPR018247 EF-Hand 1, calcium-binding site
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_007750-T1
|
-1.181450
|
IPR027417 P-loop containing nucleoside triphosphate hydrolase
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002820-T1
|
-1.183558
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_010051-T1
|
-1.184568
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_003247-T1
|
-1.184643
|
IPR001878 Zinc finger, CCHC-type, IPR025836 Zinc knuckle CX2CX4HX4C, IPR036875 Zinc finger, CCHC-type superfamily
|
NA
|
NA
|
K09250
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009621-T1
|
-1.188204
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005620-T1
|
-1.188513
|
IPR001841 Zinc finger, RING-type, IPR004331 SPX domain, IPR011016 Zinc finger, RING-CH-type, IPR013083 Zinc finger, RING/FYVE/PHD-type, IPR017907 Zinc finger, RING-type, conserved site
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_009321-T1
|
-1.190228
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_003448-T1
|
-1.191987
|
NA
|
NA
|
NA
|
|
TRUE
|
TRUE
|
|
XANPAGTX0501_009141-T1
|
-1.192722
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009887-T1
|
-1.200786
|
NA
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_000610-T1
|
-1.207426
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001643-T1
|
-1.215746
|
IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily, IPR036047 F-box-like domain superfamily
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_010380-T1
|
-1.223224
|
IPR000210 BTB/POZ domain, IPR011333 SKP1/BTB/POZ domain superfamily
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_007403-T1
|
-1.228285
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_001082-T1
|
-1.232060
|
IPR004853 Sugar phosphate transporter domain
|
NA
|
NA
|
K26222
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004416-T1
|
-1.234261
|
IPR000246 Peptidase T2, asparaginase 2, IPR029055 Nucleophile aminohydrolases, N-terminal, IPR037464 Threonine aspartase 1
|
NA
|
T02
|
K08657
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001064-T1
|
-1.234644
|
IPR021765 Mycotoxin biosynthesis protein UstYa-like
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001061-T1
|
-1.235309
|
IPR002328 Alcohol dehydrogenase, zinc-type, conserved site, IPR011032 GroES-like superfamily, IPR013149 Alcohol dehydrogenase-like, C-terminal, IPR013154 Alcohol dehydrogenase-like, N-terminal, IPR020843 Polyketide synthase, enoylreductase domain, IPR036291 NAD(P)-binding domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004018-T2
|
-1.235695
|
IPR011009 Protein kinase-like domain superfamily, IPR016477 Fructosamine/Ketosamine-3-kinase
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_007231-T1
|
-1.240318
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009316-T1
|
-1.246011
|
IPR001810 F-box domain, IPR036047 F-box-like domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_003283-T1
|
-1.246856
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_007244-T1
|
-1.249898
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008533-T1
|
-1.253515
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_007343-T1
|
-1.255419
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001952-T1
|
-1.257146
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001950-T1
|
-1.259001
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002213-T1
|
-1.262177
|
IPR000629 ATP-dependent RNA helicase DEAD-box, conserved site, IPR001650 Helicase, C-terminal, IPR011545 DEAD/DEAH box helicase domain, IPR014001 Helicase superfamily 1/2, ATP-binding domain, IPR014014 RNA helicase, DEAD-box type, Q motif, IPR027417 P-loop containing nucleoside triphosphate hydrolase
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001951-T1
|
-1.262779
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000604-T1
|
-1.264223
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_010117-T1
|
-1.267941
|
IPR002110 Ankyrin repeat, IPR011009 Protein kinase-like domain superfamily, IPR016477 Fructosamine/Ketosamine-3-kinase, IPR020683 Domain of unknown function DUF3447, IPR036770 Ankyrin repeat-containing domain superfamily
|
NA
|
NA
|
K15523
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000697-T1
|
-1.273117
|
NA
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_008628-T1
|
-1.274944
|
IPR023346 Lysozyme-like domain superfamily
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_001956-T1
|
-1.276631
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000398-T1
|
-1.277824
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002057-T1
|
-1.282644
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001888-T1
|
-1.289043
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006449-T1
|
-1.291222
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008008-T1
|
-1.291576
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_003282-T1
|
-1.293552
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008426-T1
|
-1.294283
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005613-T1
|
-1.294861
|
IPR003615 HNH nuclease
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_007464-T1
|
-1.298109
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_007870-T1
|
-1.300798
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006245-T1
|
-1.301264
|
NA
|
NA
|
NA
|
|
TRUE
|
TRUE
|
|
XANPAGTX0501_008420-T1
|
-1.301707
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001947-T1
|
-1.303157
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006330-T1
|
-1.307915
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000892-T1
|
-1.309666
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_010304-T1
|
-1.314210
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001362-T1
|
-1.314577
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004628-T1
|
-1.317480
|
IPR002156 Ribonuclease H domain, IPR012337 Ribonuclease H-like superfamily, IPR036397 Ribonuclease H superfamily
|
NA
|
NA
|
K03469
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001330-T1
|
-1.320530
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_005658-T1
|
-1.322458
|
IPR001153 Barwin domain, IPR009009 RlpA-like protein, double-psi beta-barrel domain, IPR036908 RlpA-like domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005402-T1
|
-1.324043
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_002165-T1
|
-1.325802
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008534-T1
|
-1.327391
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002170-T1
|
-1.328820
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009317-T1
|
-1.330469
|
IPR008979 Galactose-binding-like domain superfamily
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_005394-T1
|
-1.334492
|
IPR002575 Aminoglycoside phosphotransferase, IPR011009 Protein kinase-like domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005631-T1
|
-1.336475
|
IPR023631 Amidase signature domain, IPR036928 Amidase signature (AS) superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002103-T1
|
-1.336659
|
IPR036910 High mobility group box domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008856-T1
|
-1.339511
|
IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_000681-T1
|
-1.344215
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002185-T1
|
-1.352061
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_003775-T1
|
-1.352148
|
IPR003100 PAZ domain, IPR003165 Piwi domain, IPR012337 Ribonuclease H-like superfamily, IPR014811 Argonaute, linker 1 domain, IPR032472 Argonaute linker 2 domain, IPR032473 Protein argonaute, Mid domain, IPR032474 Protein argonaute, N-terminal, IPR036085 PAZ domain superfamily, IPR036397 Ribonuclease H superfamily
|
NA
|
NA
|
K11593
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004580-T1
|
-1.355977
|
IPR007292 Nuclear fusion protein Kar5
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001010-T1
|
-1.356734
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002104-T1
|
-1.360844
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004494-T1
|
-1.362189
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001859-T1
|
-1.367755
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_000025-T1
|
-1.368135
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_005597-T1
|
-1.371604
|
IPR006421 Glycogen debranching enzyme, metazoa, IPR008928 Six-hairpin glycosidase superfamily, IPR012341 Six-hairpin glycosidase-like superfamily, IPR017853 Glycoside hydrolase superfamily, IPR029436 Eukaryotic glycogen debranching enzyme, N-terminal domain, IPR032788 Glycogen debranching enzyme, central domain, IPR032790 Glycogen debranching enzyme, C-terminal, IPR032792 Glycogen debranching enzyme, glucanotransferase domain
|
GH133
|
NA
|
K01196
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004950-T1
|
-1.372326
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005048-T1
|
-1.374486
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004217-T1
|
-1.376777
|
IPR000504 RNA recognition motif domain, IPR012677 Nucleotide-binding alpha-beta plait domain superfamily, IPR035979 RNA-binding domain superfamily
|
NA
|
NA
|
K24990
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000005-T1
|
-1.378844
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_003212-T1
|
-1.384927
|
IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily, IPR036047 F-box-like domain superfamily
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_002763-T1
|
-1.389644
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002163-T1
|
-1.392989
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_003213-T1
|
-1.399730
|
IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily, IPR036047 F-box-like domain superfamily
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_004493-T1
|
-1.400770
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002166-T1
|
-1.400943
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_010280-T1
|
-1.404057
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006016-T1
|
-1.404604
|
IPR008928 Six-hairpin glycosidase superfamily, IPR031335 Glycosyl hydrolase family 63, C-terminal
|
GH63
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001333-T1
|
-1.411305
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_004104-T1
|
-1.419256
|
IPR001214 SET domain, IPR011990 Tetratricopeptide-like helical domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_007067-T1
|
-1.420720
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_007300-T1
|
-1.423032
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004414-T1
|
-1.423458
|
IPR027417 P-loop containing nucleoside triphosphate hydrolase
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_001605-T1
|
-1.425833
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006255-T1
|
-1.434751
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000647-T1
|
-1.440550
|
IPR000571 Zinc finger, CCCH-type
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005615-T1
|
-1.440903
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006974-T1
|
-1.441975
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006957-T1
|
-1.443602
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006910-T1
|
-1.458293
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001612-T1
|
-1.458506
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_007871-T1
|
-1.463016
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_009582-T1
|
-1.469666
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009615-T1
|
-1.478640
|
IPR035940 CAP superfamily
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_001953-T1
|
-1.483265
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009139-T1
|
-1.494375
|
IPR001876 Zinc finger, RanBP2-type
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005630-T1
|
-1.497428
|
IPR036928 Amidase signature (AS) superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004891-T1
|
-1.501545
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002522-T1
|
-1.504550
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005612-T1
|
-1.506602
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_000893-T1
|
-1.508341
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005061-T1
|
-1.508665
|
NA
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_007873-T1
|
-1.510868
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_001958-T1
|
-1.511188
|
IPR001356 Homeobox domain, IPR009057 Homeobox-like domain superfamily, IPR017970 Homeobox, conserved site
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000194-T1
|
-1.511338
|
IPR006047 Glycosyl hydrolase, family 13, catalytic domain, IPR013780 Glycosyl hydrolase, all-beta, IPR017853 Glycoside hydrolase superfamily
|
GH13
|
NA
|
K01176
|
FALSE
|
FALSE
|
|
XANPAGTX0501_003572-T1
|
-1.519271
|
IPR001087 GDSL lipase/esterase, IPR036514 SGNH hydrolase superfamily
|
CE16
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_002183-T1
|
-1.522262
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005279-T1
|
-1.523896
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008041-T1
|
-1.527220
|
NA
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_005614-T1
|
-1.527719
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001538-T1
|
-1.528884
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001954-T1
|
-1.534783
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001414-T1
|
-1.537299
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001910-T1
|
-1.539771
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_010303-T1
|
-1.542026
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004520-T1
|
-1.559567
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_007262-T1
|
-1.569541
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_010203-T1
|
-1.569541
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_008090-T1
|
-1.570035
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009318-T1
|
-1.577677
|
IPR011333 SKP1/BTB/POZ domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002164-T1
|
-1.582652
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002184-T1
|
-1.584723
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005735-T1
|
-1.620055
|
IPR018824 Conidiation-specific protein 6
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004521-T1
|
-1.625040
|
IPR008271 Serine/threonine-protein kinase, active site, IPR011009 Protein kinase-like domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002172-T1
|
-1.626040
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001967-T1
|
-1.629031
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008009-T1
|
-1.631945
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009605-T1
|
-1.639551
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009619-T1
|
-1.640066
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001611-T1
|
-1.646921
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005766-T1
|
-1.650350
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_002182-T1
|
-1.670548
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008782-T1
|
-1.681484
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009786-T1
|
-1.691780
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001962-T1
|
-1.692967
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_007872-T1
|
-1.694556
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_006253-T1
|
-1.695976
|
IPR014849 EKC/KEOPS complex, subunit Gon7
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008331-T1
|
-1.707064
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_003209-T1
|
-1.709229
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_000193-T1
|
-1.729825
|
IPR006047 Glycosyl hydrolase, family 13, catalytic domain, IPR017853 Glycoside hydrolase superfamily
|
GH13
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001960-T1
|
-1.733269
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_006951-T1
|
-1.742660
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008007-T1
|
-1.745209
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_010596-T1
|
-1.748698
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_005814-T1
|
-1.760286
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008284-T1
|
-1.771059
|
IPR029044 Nucleotide-diphospho-sugar transferases
|
GT2_Glyco_tranf_2
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009926-T1
|
-1.775143
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_009602-T1
|
-1.777131
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001063-T1
|
-1.783787
|
NA
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_007397-T1
|
-1.849425
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_007900-T1
|
-1.867603
|
NA
|
NA
|
NA
|
|
FALSE
|
TRUE
|
|
XANPAGTX0501_000378-T1
|
-1.880561
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004966-T1
|
-1.889077
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001856-T1
|
-1.894636
|
IPR037176 Osmotin/thaumatin-like superfamily
|
NA
|
NA
|
|
TRUE
|
TRUE
|
|
XANPAGTX0501_006327-T1
|
-1.922253
|
IPR018466 Yeast cell wall synthesis Kre9/Knh1-like, N-terminal
|
NA
|
NA
|
|
TRUE
|
FALSE
|
|
XANPAGTX0501_002506-T1
|
-1.931043
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_003211-T1
|
-2.074356
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_008109-T1
|
-2.159140
|
IPR004143 Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain
|
NA
|
NA
|
K03800
|
FALSE
|
FALSE
|
|
XANPAGTX0501_004085-T1
|
-2.298435
|
IPR000420 Yeast PIR protein repeat
|
NA
|
NA
|
K26550
|
TRUE
|
FALSE
|
|
XANPAGTX0501_008519-T2
|
-2.955922
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
|
XANPAGTX0501_001156-T3
|
-3.105399
|
IPR003822 Paired amphipathic helix, IPR013194 Histone deacetylase interacting domain, IPR031693 Sin3, C-terminal, IPR036600 Paired amphipathic helix superfamily
|
NA
|
NA
|
K11644
|
FALSE
|
FALSE
|
- Selected only genes that are potentially multicellularity related
mult_gene_table_ap3<-mult_gene_table %>% inner_join(a_sig %>% filter(change=="apothecium") %>% select(target_id,b),by=c("TranscriptID"="target_id")) %>% arrange(Function)
mult_gene_table_ap3 %>%
kable(format = "html", col.names = colnames(mult_gene_table_ap3)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
|
TranscriptID
|
ID
|
Annotation_type
|
Description
|
Function
|
Function_type
|
b
|
|
XANPAGTX0501_001061-T1
|
IPR013149
|
IPR
|
Alcohol dehydrogenase-like, C-terminal
|
Acetyl-CoA production and metabolism
|
Fungal multicellularity
|
-1.235309
|
|
XANPAGTX0501_005597-T1
|
IPR032788
|
IPR
|
Glycogen debranching enzyme, central domain
|
Carbohydrate storage
|
Fungal multicellularity
|
-1.371604
|
|
XANPAGTX0501_000647-T1
|
IPR000571
|
IPR
|
Zinc finger, CCCH-type
|
Cell division, proliferation and growth
|
Fungal multicellularity
|
-1.440550
|
|
XANPAGTX0501_002213-T1
|
IPR001650
|
IPR
|
Helicase, C-terminal
|
Cell division, proliferation and growth
|
Fungal multicellularity
|
-1.262177
|
|
XANPAGTX0501_003775-T1
|
IPR012337
|
IPR
|
Ribonuclease H-like superfamily
|
Cell division, proliferation and growth
|
Fungal multicellularity
|
-1.352148
|
|
XANPAGTX0501_003775-T2
|
IPR012337
|
IPR
|
Ribonuclease H-like superfamily
|
Cell division, proliferation and growth
|
Fungal multicellularity
|
-1.015597
|
|
XANPAGTX0501_004104-T1
|
IPR001214
|
IPR
|
SET domain
|
Cell division, proliferation and growth
|
Fungal multicellularity
|
-1.419256
|
|
XANPAGTX0501_004628-T1
|
IPR012337
|
IPR
|
Ribonuclease H-like superfamily
|
Cell division, proliferation and growth
|
Fungal multicellularity
|
-1.317480
|
|
XANPAGTX0501_003124-T1
|
IPR001461
|
IPR
|
Aspartic peptidase A1 family
|
Cell surface and cell wall proteins
|
Fungal multicellularity
|
-1.035285
|
|
XANPAGTX0501_005735-T1
|
IPR018824
|
IPR
|
Conidiation-specific protein 6
|
Cell surface and cell wall proteins
|
Fungal multicellularity
|
-1.620055
|
|
XANPAGTX0501_006327-T1
|
IPR018466
|
IPR
|
Yeast cell wall synthesis Kre9/Knh1-like, N-terminal
|
Cell wall biosynthesis
|
Fungal multicellularity
|
-1.922253
|
|
XANPAGTX0501_001856-T1
|
IPR037176
|
IPR
|
Osmotin/thaumatin-like superfamily
|
Cell wall remodeling
|
Fungal multicellularity
|
-1.894636
|
|
XANPAGTX0501_007833-T1
|
IPR002889
|
IPR
|
Carbohydrate-binding WSC
|
Cell wall remodeling
|
Fungal multicellularity
|
-1.003237
|
|
XANPAGTX0501_009511-T1
|
GH16
|
CAZy
|
act on beta-1,4 or beta-1,3 glycosidic bonds in glucans and galactans
|
Cell wall remodeling
|
Fungal multicellularity
|
-1.136478
|
|
XANPAGTX0501_001064-T1
|
IPR021765
|
IPR
|
Mycotoxin biosynthesis protein UstYa-like
|
Defense
|
Fungal multicellularity
|
-1.234644
|
|
XANPAGTX0501_001643-T1
|
IPR001810
|
IPR
|
F-box domain
|
Protein ubiquitination
|
Fungal multicellularity
|
-1.215746
|
|
XANPAGTX0501_003212-T1
|
IPR001810
|
IPR
|
F-box domain
|
Protein ubiquitination
|
Fungal multicellularity
|
-1.384927
|
|
XANPAGTX0501_003213-T1
|
IPR001810
|
IPR
|
F-box domain
|
Protein ubiquitination
|
Fungal multicellularity
|
-1.399730
|
|
XANPAGTX0501_005620-T1
|
IPR017907
|
IPR
|
Zinc finger; RING-type; conserved site
|
Protein ubiquitination
|
Fungal multicellularity
|
-1.188513
|
|
XANPAGTX0501_005815-T1
|
IPR000210
|
IPR
|
BTB/POZ domain
|
Protein ubiquitination
|
Fungal multicellularity
|
-1.064277
|
|
XANPAGTX0501_006203-T1
|
IPR017907
|
IPR
|
Zinc finger; RING-type; conserved site
|
Protein ubiquitination
|
Fungal multicellularity
|
-1.175049
|
|
XANPAGTX0501_007869-T1
|
IPR000210
|
IPR
|
BTB/POZ domain
|
Protein ubiquitination
|
Fungal multicellularity
|
-1.136332
|
|
XANPAGTX0501_008856-T1
|
IPR001810
|
IPR
|
F-box domain
|
Protein ubiquitination
|
Fungal multicellularity
|
-1.339511
|
|
XANPAGTX0501_009316-T1
|
IPR001810
|
IPR
|
F-box domain
|
Protein ubiquitination
|
Fungal multicellularity
|
-1.246011
|
|
XANPAGTX0501_009942-T1
|
IPR001810
|
IPR
|
F-box domain
|
Protein ubiquitination
|
Fungal multicellularity
|
-1.164912
|
|
XANPAGTX0501_010380-T1
|
IPR000210
|
IPR
|
BTB/POZ domain
|
Protein ubiquitination
|
Fungal multicellularity
|
-1.223224
|
|
XANPAGTX0501_002098-T1
|
IPR000504
|
IPR
|
RNA recognition motif domain
|
RNA binding proteins
|
Expression regulation
|
-1.056175
|
|
XANPAGTX0501_002123-T1
|
IPR000504
|
IPR
|
RNA recognition motif domain
|
RNA binding proteins
|
Expression regulation
|
-1.092697
|
|
XANPAGTX0501_004217-T1
|
IPR000504
|
IPR
|
RNA recognition motif domain
|
RNA binding proteins
|
Expression regulation
|
-1.376777
|
|
XANPAGTX0501_002123-T1
|
IPR007855
|
IPR
|
RNA-dependent RNA polymerase, eukaryotic-type
|
RNA interference
|
Expression regulation
|
-1.092697
|
|
XANPAGTX0501_003775-T1
|
IPR032474
|
IPR
|
Protein argonaute, N-terminal
|
RNA interference
|
Expression regulation
|
-1.352148
|
|
XANPAGTX0501_003775-T2
|
IPR032474
|
IPR
|
Protein argonaute, N-terminal
|
RNA interference
|
Expression regulation
|
-1.015597
|
|
XANPAGTX0501_000420-T1
|
IPR013087
|
IPR
|
Zinc finger C2H2-type
|
Transcription factors
|
Expression regulation
|
-1.104047
|
|
XANPAGTX0501_001955-T1
|
IPR036864
|
IPR
|
Zn(2)-C6 fungal-type DNA-binding domain superfamily
|
Transcription factors
|
Expression regulation
|
-1.028447
|
|
XANPAGTX0501_001958-T1
|
IPR001356
|
IPR
|
Homeobox domain
|
Transcription factors
|
Expression regulation
|
-1.511188
|
|
XANPAGTX0501_005620-T1
|
IPR013083
|
IPR
|
Zinc finger, RING/FYVE/PHD-type
|
Transcription factors
|
Expression regulation
|
-1.188513
|
|
XANPAGTX0501_006203-T1
|
IPR013083
|
IPR
|
Zinc finger, RING/FYVE/PHD-type
|
Transcription factors
|
Expression regulation
|
-1.175049
|
|
XANPAGTX0501_001825-T1
|
IPR036259
|
IPR
|
MFS transporter superfamily
|
Transporters
|
Fungal multicellularity
|
-1.063406
|
###enrichment analysis
enrich<-clusterProfiler::enricher(ap_a_genes$target_id,
pAdjustMethod = "none",
minGSSize = 1,
maxGSSize = 2000,
qvalueCutoff = 1,
universe=ips_data$universe,
TERM2GENE=ips_data$term2protein,
TERM2NAME=ips_data$term2name)
enrich_pairwise<-enrichplot::pairwise_termsim(enrich)
enrichplot::emapplot(enrich_pairwise)

pdf(file="../results/apothecia_upr.pdf",width=6,height=5)
enrichplot::emapplot(enrich_pairwise,cex_label_category=0.4,cex_line=0.25,
shadowtext=F,cex_pie2axis=0.1,repel=T)
dev.off()
## quartz_off_screen
## 2
- This new set includes almost all of the genes from the center/apothecia comparison. It also includes 59% of the genes from the edge/apothecia comparison. It also includes 12 genes unique to this set
venn_a2<-list(compared_to_center = ca_sig$target_id[ca_sig$change=="apothecium"],
compared_to_edge = ea_sig$target_id[ea_sig$change=="apothecium"],
compared_to_center_edge_pooled=a_sig$target_id[a_sig$change=="apothecium"])
a2<-ggVennDiagram(venn_a2,label_size = 5,set_size=5)+labs(title = "Upregulated in apothecia")+theme(title=element_text(size=12))+scale_x_continuous(expand = expansion(mult = .4))
a2

7. Visualize MAT expression
- Standartd heatmap - not very clear
library(ComplexHeatmap)
library(viridis)
#make a matrix
tabd_df_a <- a_so$obs_norm[a_so$obs_norm$target_id %in% target_id,]
tabd_df_a <- dplyr::select(tabd_df_a, target_id, sample,
tpm)
tabd_df_a <- reshape2::dcast(tabd_df_a, target_id ~ sample,
value.var = "tpm")
rownames(tabd_df_a) <- tabd_df_a$target_id
tabd_df_a$target_id <- NULL
trans_mat_a <- as.matrix(log(tabd_df_a + 1))
#make a top annotation
#define column annotations
s2c_a <- a_so$sample_to_covariates
s2c_a<-data.frame("sample"= colnames(tabd_df_a)) %>% left_join(s2c_a)
rownames(s2c_a)<-s2c_a$sample
s2c_a<-s2c_a %>% select(part)
ta_colors_a = c("apothecia" = "#619CFF", "thallus_edge" = "#F8766D","thallus_centre"="green")
ta_a = HeatmapAnnotation(df=s2c_a,col = list(condition = ta_colors_a))
#filter to include only MAT locus
filt_mat_MAT<-subset(trans_mat_a, rownames(trans_mat_a) %in% c("XANPAGTX0501_002103-T1","XANPAGTX0501_002104-T1"))
HM_mat = Heatmap(filt_mat_MAT, show_row_names = T, show_column_names = T,cluster_rows = T, row_title_rot = 0, col=viridis(100), heatmap_legend_param = list(title = "Expression: log(TPM)"), top_annotation = ta_a)
pdf(file="../results/MAT_heatmap.pdf",width=10,height=2)
draw(HM_mat)
dev.off()
## quartz_off_screen
## 2
HM_mat
* lolipop plot arranged by specimen
df<-data.frame(filt_mat_MAT) %>% mutate(target_id=rownames(filt_mat_MAT)) %>%
pivot_longer(-target_id,names_to="sample",values_to="expression") %>% left_join(a_so$sample_to_covariates)
write.table(df, file="../analysis_and_temp_files/09_dge_architecture/mat_expression.txt", quote=F, sep='\t', row.names=F)
#only include thalli that a. have apothecia sample and b. have at least two samples
incl<-a_so$sample_to_covariates %>% mutate(if_apothecia=ifelse(part=="apothecia",T,F)) %>%
group_by(thallus) %>% summarize(n=n(),n_ap=sum(if_apothecia)) %>% filter(n>1,n_ap>0)
gg<-ggplot(df %>% filter(thallus %in% incl$thallus), aes(color=part,y=expression,x=part))+
geom_segment( aes(x=part, xend=part, y=0, yend=expression))+
geom_point(stat = "identity",position=position_dodge(width = .5))+
facet_grid(target_id~thallus)+
xlab("")+ylab("Expression: log(TPM)")+
theme_bw()+ scale_x_discrete(guide = guide_axis(angle = 45))+
scale_color_manual( values = color_scheme)+
theme(text=element_text(size=6),legend.position="bottom")
ggsave('../results/MAT_lopipop.pdf',gg, width = 4, height = 3)
gg

Investigate the most apothecia-upregulated proteins
- XANPAGTX0501_001156-T3 is one variant of Sin3 transcriptional regulator
- Only one is upregulated
filt_mat_sin3<-subset(trans_mat_a, rownames(trans_mat_a) %in% c("XANPAGTX0501_001156-T1","XANPAGTX0501_001156-T2","XANPAGTX0501_001156-T3"))
HM_sin3 = Heatmap(filt_mat_sin3, show_row_names = T, show_column_names = T,cluster_rows = T, row_title_rot = 0, col=viridis(100), heatmap_legend_param = list(title = "Expression: log(TPM)"), top_annotation = ta_a)
draw(HM_sin3)

df_sin3<-data.frame(filt_mat_sin3) %>% mutate(target_id=rownames(filt_mat_sin3)) %>%
pivot_longer(-target_id,names_to="sample",values_to="expression") %>% left_join(a_so$sample_to_covariates)
## Joining with `by = join_by(sample)`
ggplot(df_sin3 %>% filter(thallus %in% incl$thallus), aes(color=part,y=expression,x=part))+
geom_segment( aes(x=part, xend=part, y=0, yend=expression))+
geom_point(stat = "identity",position=position_dodge(width = .5))+
facet_grid(target_id~thallus)+
xlab("")+ylab("Expression: log(TPM)")+
scale_color_manual( values = color_scheme)+
theme_bw()+ scale_x_discrete(guide = guide_axis(angle = 45))

This is very interesting, but also inconsistent. Looked at the bam file but it didn’t clarify much
Visualize several key gene for the suppl. figure
- XANPAGTX0501_004521-T1: Serine/threonine-protein kinase
- XANPAGTX0501_001958-T1: Homeobox domain
- XANPAGTX0501_003775-T1,XANPAGTX0501_004244-T1: argonaute
- XANPAGTX0501_002123-T1: RNA-dependent RNA polymerase
- XANPAGTX0501_004580-T1: Nuclear fusion protein Kar5
- XANPAGTX0501_005735-T1: Conidiation-specific protein 6
- XANPAGTX0501_004217-T1, XANPAGTX0501_002123-T1, XANPAGTX0501_002098-T1: RNA-binding domain
- XANPAGTX0501_003213-T1, XANPAGTX0501_008856-T1, XANPAGTX0501_009316-T1, XANPAGTX0501_009942-T1, XANPAGTX0501_003212-T1, XANPAGTX0501_001643-T1: F-box
- XANPAGTX0501_005815-T1,XANPAGTX0501_007869-T1,XANPAGTX0501_010380-T1: POZ
library(patchwork)
ap_genes<-c("XANPAGTX0501_004521-T1","XANPAGTX0501_001958-T1","XANPAGTX0501_004580-T1","XANPAGTX0501_005735-T1","XANPAGTX0501_002123-T1","XANPAGTX0501_003775-T1","XANPAGTX0501_004244-T1","XANPAGTX0501_004217-T1", "XANPAGTX0501_002098-T1")
filt_mat_ap<-subset(trans_mat_a, rownames(trans_mat_a) %in% ap_genes)
df_ap<-data.frame(filt_mat_ap) %>% mutate(target_id=rownames(filt_mat_ap)) %>%
pivot_longer(-target_id,names_to="sample",values_to="expression") %>% left_join(a_so$sample_to_covariates)
df_ap$target_id<-factor(df_ap$target_id,levels=c("XANPAGTX0501_004521-T1","XANPAGTX0501_001958-T1","XANPAGTX0501_004580-T1","XANPAGTX0501_005735-T1","XANPAGTX0501_002123-T1","XANPAGTX0501_003775-T1","XANPAGTX0501_004244-T1",
"XANPAGTX0501_004217-T1", "XANPAGTX0501_002098-T1") )
gg_ap<-ggplot(df_ap %>% filter(thallus %in% incl$thallus), aes(color=part,y=expression,x=part))+
geom_segment( aes(x=part, xend=part, y=0, yend=expression))+
geom_point(stat = "identity",position=position_dodge(width = .5))+
facet_grid(target_id~thallus)+
xlab("")+ylab("Expression: log(TPM)")+
theme_bw()+ scale_x_discrete(guide = guide_axis(angle = 45))+
scale_color_manual( values = color_scheme)+
theme(text=element_text(size=6))
ap_genes2<-c("XANPAGTX0501_003213-T1", "XANPAGTX0501_008856-T1", "XANPAGTX0501_009316-T1","XANPAGTX0501_009942-T1", "XANPAGTX0501_003212-T1", "XANPAGTX0501_001643-T1","XANPAGTX0501_005815-T1","XANPAGTX0501_007869-T1",
"XANPAGTX0501_010380-T1")
filt_mat_ap2<-subset(trans_mat_a, rownames(trans_mat_a) %in% ap_genes2)
df_ap2<-data.frame(filt_mat_ap2) %>% mutate(target_id=rownames(filt_mat_ap2)) %>%
pivot_longer(-target_id,names_to="sample",values_to="expression") %>% left_join(a_so$sample_to_covariates)
df_ap2$target_id<-factor(df_ap2$target_id,levels=c("XANPAGTX0501_003213-T1", "XANPAGTX0501_008856-T1", "XANPAGTX0501_009316-T1","XANPAGTX0501_009942-T1", "XANPAGTX0501_003212-T1", "XANPAGTX0501_001643-T1","XANPAGTX0501_005815-T1","XANPAGTX0501_007869-T1",
"XANPAGTX0501_010380-T1") )
gg_ap2<-ggplot(df_ap2 %>% filter(thallus %in% incl$thallus), aes(color=part,y=expression,x=part))+
geom_segment( aes(x=part, xend=part, y=0, yend=expression))+
geom_point(stat = "identity",position=position_dodge(width = .5))+
facet_grid(target_id~thallus)+
xlab("")+ylab("")+
theme_bw()+ scale_x_discrete(guide = guide_axis(angle = 45)) +
scale_color_manual( values = color_scheme)+
theme(text=element_text(size=6))
gg_ap_all<-gg_ap+gg_ap2+ plot_layout(axis_titles = "collect",guides = 'collect')
ggsave('../results/apothecia_dge_lopipop.pdf',gg_ap_all, width = 8, height = 10)
- Visualize a couple most interesting for the main figure on apothecia
#get the matrix for all samples, including culture
tabd_df<-read.delim2("../analysis_and_temp_files/08_dge_culture_lichen/norm_counts_sleuth.txt")
rownames(tabd_df) <- tabd_df$target_id
tabd_df$target_id <- NULL
tabd_df <- mutate_all(tabd_df, function(x) as.numeric(as.character(x)))
trans_mat_08 <- as.matrix(log(tabd_df + 1))
selected_genes<-c("XANPAGTX0501_008856-T1","XANPAGTX0501_002123-T1")
#graph for the lichen samples
filt_mat_selected_thalli<-subset(trans_mat_a, rownames(trans_mat_a) %in% selected_genes)
df_thalli<-data.frame(filt_mat_selected_thalli) %>% mutate(target_id=rownames(filt_mat_selected_thalli)) %>%
pivot_longer(-target_id,names_to="sample",values_to="expression") %>% left_join(a_so$sample_to_covariates)
## Joining with `by = join_by(sample)`
df_thalli$target_id<-factor(df_thalli$target_id,levels=c("XANPAGTX0501_008856-T1","XANPAGTX0501_002123-T1"))
gg_selected_thalli<-ggplot(df_thalli %>% filter(thallus %in% incl$thallus), aes(color=part,y=expression,x=part))+
geom_segment( aes(x=part, xend=part, y=0, yend=expression))+
geom_point(stat = "identity",position=position_dodge(width = .5))+
facet_grid(target_id~thallus)+
xlab("")+ylab("Expression: log(TPM)")+
theme_bw()+ scale_x_discrete(guide = guide_axis(angle = 45)) +
scale_color_manual( values = color_scheme)+
theme(text=element_text(size=6),legend.position = "bottom",
axis.text.x = element_blank(),axis.ticks.x = element_blank())
#graph for the culture
filt_mat_selected_culture<-subset(trans_mat_08, rownames(trans_mat_08) %in% selected_genes)
df_culture<-data.frame(filt_mat_selected_culture) %>% mutate(target_id=rownames(filt_mat_selected_culture)) %>%
pivot_longer(-target_id,names_to="sample",values_to="expression") %>%
filter(!(sample %in% colnames(filt_mat_selected_thalli)))
df_culture$target_id<-factor(df_culture$target_id,levels=c("XANPAGTX0501_008856-T1","XANPAGTX0501_002123-T1"))
gg_selected_culture<-ggplot(df_culture, aes(y=expression,x=sample))+
geom_segment( aes(x=sample, xend=sample, y=0, yend=expression))+
geom_point(stat = "identity",position=position_dodge(width = .5))+
facet_grid(target_id~.)+
xlab("")+ylab("")+
theme_bw()+ scale_x_discrete(guide = guide_axis(angle = 45)) + theme(text=element_text(size=6),axis.text = element_blank(),
axis.ticks = element_blank(),
axis.title.y = element_blank() )
ggsel<-gg_selected_thalli + gg_selected_culture + plot_layout(widths = c(0.6,0.4),nrow = 1) & scale_y_continuous(limits = c(0, 2.5))
#had to make one of them separately baceaus of the axes issue
selected_genes<-c("XANPAGTX0501_003775-T1")
#graph for the lichen samples
filt_mat_selected_thalli<-subset(trans_mat_a, rownames(trans_mat_a) %in% selected_genes)
df_thalli<-data.frame(filt_mat_selected_thalli) %>% mutate(target_id=rownames(filt_mat_selected_thalli)) %>%
pivot_longer(-target_id,names_to="sample",values_to="expression") %>% left_join(a_so$sample_to_covariates)
## Joining with `by = join_by(sample)`
#df_thalli$target_id<-factor(df_selected$target_id,levels=c())
gg_selected_thalli<-ggplot(df_thalli %>% filter(thallus %in% incl$thallus), aes(color=part,y=expression,x=part))+
geom_segment( aes(x=part, xend=part, y=0, yend=expression))+
geom_point(stat = "identity",position=position_dodge(width = .5))+
facet_grid(target_id~thallus)+
xlab("")+ylab("Expression: log(TPM)")+
theme_bw()+ scale_x_discrete(guide = guide_axis(angle = 45)) +
scale_color_manual( values = color_scheme)+
theme(text=element_text(size=6),legend.position = "bottom",
strip.background.x = element_blank(),strip.text.x = element_blank())
#graph for the culture
filt_mat_selected_culture<-subset(trans_mat_08, rownames(trans_mat_08) %in% selected_genes)
df_culture<-data.frame(filt_mat_selected_culture) %>% mutate(target_id=rownames(filt_mat_selected_culture)) %>%
pivot_longer(-target_id,names_to="sample",values_to="expression") %>%
filter(!(sample %in% colnames(filt_mat_selected_thalli)))
#df_thalli$target_id<-factor(df_selected$target_id,levels=c())
gg_selected_culture<-ggplot(df_culture, aes(y=expression,x=sample))+
geom_segment( aes(x=sample, xend=sample, y=0, yend=expression))+
geom_point(stat = "identity",position=position_dodge(width = .5))+
facet_grid(target_id~.)+
xlab("")+ylab("")+
theme_bw()+ scale_x_discrete(guide = guide_axis(angle = 45)) + theme(text=element_text(size=6),axis.text.y = element_blank(),
axis.ticks.y = element_blank(),
axis.title.y = element_blank() )
ggsel2<-gg_selected_thalli + gg_selected_culture + plot_layout(widths = c(0.6,0.4),nrow = 1) & scale_y_continuous(limits = c(0, 5))
sel_final<-ggsel/plot_spacer()/ggsel2+ plot_layout(axis_titles = "collect",guides = "collect",heights = c(0.66,-0.155,0.34)) &theme(legend.position = "bottom")
ggsave('../results/selected_apothecia_dge_lopipop.pdf',sel_final, width = 7, height = 4)
sel_final

Visualize interesting edge-upregulated genes
#get the matrix for all samples, including culture
selected_genes<-c("XANPAGTX0501_009376-T1","XANPAGTX0501_008852-T1")
#graph for the lichen samples
filt_mat_selected_thalli<-subset(trans_mat_a, rownames(trans_mat_a) %in% selected_genes)
df_thalli<-data.frame(filt_mat_selected_thalli) %>% mutate(target_id=rownames(filt_mat_selected_thalli)) %>%
pivot_longer(-target_id,names_to="sample",values_to="expression") %>% left_join(a_so$sample_to_covariates)
## Joining with `by = join_by(sample)`
gg_selected_thalli<-ggplot(df_thalli %>% filter(thallus %in% incl$thallus), aes(color=part,y=expression,x=part))+
geom_segment( aes(x=part, xend=part, y=0, yend=expression))+
geom_point(stat = "identity",position=position_dodge(width = .5))+
facet_grid(target_id~thallus)+
xlab("")+ylab("Expression: log(TPM)")+
theme_bw()+ scale_x_discrete(guide = guide_axis(angle = 45)) +
scale_color_manual( values = color_scheme)+
theme(text=element_text(size=6),legend.position = "bottom",
strip.background.x = element_blank(),strip.text.x = element_blank())
#graph for the culture
filt_mat_selected_culture<-subset(trans_mat_08, rownames(trans_mat_08) %in% selected_genes)
df_culture<-data.frame(filt_mat_selected_culture) %>% mutate(target_id=rownames(filt_mat_selected_culture)) %>%
pivot_longer(-target_id,names_to="sample",values_to="expression") %>%
filter(!(sample %in% colnames(filt_mat_selected_thalli)))
gg_selected_culture<-ggplot(df_culture, aes(y=expression,x=sample))+
geom_segment( aes(x=sample, xend=sample, y=0, yend=expression))+
geom_point(stat = "identity",position=position_dodge(width = .5))+
facet_grid(target_id~.)+
xlab("")+ylab("")+
theme_bw()+ scale_x_discrete(guide = guide_axis(angle = 45)) + theme(text=element_text(size=6),axis.text.y = element_blank(),
axis.ticks.y = element_blank(),
axis.title.y = element_blank() )
ggsel<-gg_selected_thalli + gg_selected_culture + plot_layout(widths = c(0.6,0.4),nrow = 1) & scale_y_continuous(limits = c(0, 5))
#had to make one of them separately baceaus of the axes issue
selected_genes<-c("XANPAGTX0501_001015-T1")
selected_genes<-c("XANPAGTX0501_001643-T1")
#graph for the lichen samples
filt_mat_selected_thalli<-subset(trans_mat_a, rownames(trans_mat_a) %in% selected_genes)
df_thalli<-data.frame(filt_mat_selected_thalli) %>% mutate(target_id=rownames(filt_mat_selected_thalli)) %>%
pivot_longer(-target_id,names_to="sample",values_to="expression") %>% left_join(a_so$sample_to_covariates)
## Joining with `by = join_by(sample)`
gg_selected_thalli<-ggplot(df_thalli %>% filter(thallus %in% incl$thallus), aes(color=part,y=expression,x=part))+
geom_segment( aes(x=part, xend=part, y=0, yend=expression))+
geom_point(stat = "identity",position=position_dodge(width = .5))+
facet_grid(target_id~thallus)+
xlab("")+ylab("Expression: log(TPM)")+
theme_bw()+ scale_x_discrete(guide = guide_axis(angle = 45)) +
scale_color_manual( values = color_scheme)+
theme(text=element_text(size=6),legend.position = "bottom",
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
axis.title.x = element_blank() )
#graph for the culture
filt_mat_selected_culture<-subset(trans_mat_08, rownames(trans_mat_08) %in% selected_genes)
df_culture<-data.frame(filt_mat_selected_culture) %>% mutate(target_id=rownames(filt_mat_selected_culture)) %>%
pivot_longer(-target_id,names_to="sample",values_to="expression") %>%
filter(!(sample %in% colnames(filt_mat_selected_thalli)))
#df_thalli$target_id<-factor(df_selected$target_id,levels=c())
gg_selected_culture<-ggplot(df_culture, aes(y=expression,x=sample))+
geom_segment( aes(x=sample, xend=sample, y=0, yend=expression))+
geom_point(stat = "identity",position=position_dodge(width = .5))+
facet_grid(target_id~.)+
xlab("")+ylab("")+
theme_bw()+ scale_x_discrete(guide = guide_axis(angle = 45)) + theme(text=element_text(size=6),axis.text = element_blank(),
axis.ticks = element_blank(),
axis.title = element_blank() )
ggsel2<-gg_selected_thalli + gg_selected_culture + plot_layout(widths = c(0.6,0.4),nrow = 1) & scale_y_continuous(limits = c(0, 7))
sel_final<-ggsel2/plot_spacer()/ggsel+ plot_layout(axis_titles = "collect",guides = "collect",heights = c(0.34,-0.105,0.66)) &theme(legend.position = "bottom")
ggsave('../results/selected_edge_dge_lopipop.pdf',sel_final, width = 7, height = 4)
sel_final

7. Compiling DGE table
ec_sig$Comparison<-"Edge / Center"
ea_sig$Comparison<-"Edge / Apothecia"
ca_sig$Comparison<-"Center / Apothecia"
a_sig$Comparison<-"Apothecia / Vegetative (edge + center)"
compiled<-rbind(ec_sig,ea_sig,ca_sig,a_sig) %>% filter(change!="low_logFC") %>%
left_join(funannot2,by=c("target_id"="TranscriptID")) %>%
select(Comparison,change,target_id,b,InterPro_new,CAZyme_new,Protease_new,KO,secreted_consensus,lichen_ortho) %>% arrange(change) %>% arrange(Comparison)
write.table(compiled, file="../results/tissue_dge.txt", quote=F, sep='\t', row.names=F)
The gene that are upregulated in the center compared to the edge, are they also apothecia-upregulated?
- All of them are at least in one apothecia-upregulated list
apothecia_up<-compiled$target_id[compiled$change=="apothecium"]
center_up<-ec_sig$target_id[ec_sig$change=="centre"]
ec_sig %>% filter(change=="centre") %>%
mutate(apothecia_upregulated = ifelse(target_id %in%apothecia_up,T,F)) %>%
select(target_id,apothecia_upregulated,b)
## # A tibble: 9 × 3
## target_id apothecia_upregulated b
## <chr> <lgl> <dbl>
## 1 XANPAGTX0501_005615-T1 TRUE -1.01
## 2 XANPAGTX0501_005614-T1 TRUE -1.08
## 3 XANPAGTX0501_008007-T1 TRUE -1.16
## 4 XANPAGTX0501_002184-T1 TRUE -1.17
## 5 XANPAGTX0501_001949-T1 TRUE -1.19
## 6 XANPAGTX0501_002506-T1 TRUE -1.19
## 7 XANPAGTX0501_008856-T1 TRUE -1.28
## 8 XANPAGTX0501_009886-T1 TRUE -1.29
## 9 XANPAGTX0501_009927-T1 TRUE -1.62
- All of them were in the apothecia/edge list
compiled %>% filter(change=="apothecium", target_id %in% center_up) %>%
select(target_id,Comparison) %>% mutate(presence=1) %>%
pivot_wider(names_from = Comparison,values_from = presence, values_fill=0)
## # A tibble: 9 × 4
## target_id Apothecia / Vegetati…¹ `Center / Apothecia` `Edge / Apothecia`
## <chr> <dbl> <dbl> <dbl>
## 1 XANPAGTX0501_0… 1 0 1
## 2 XANPAGTX0501_0… 1 1 1
## 3 XANPAGTX0501_0… 1 0 1
## 4 XANPAGTX0501_0… 1 1 1
## 5 XANPAGTX0501_0… 1 1 1
## 6 XANPAGTX0501_0… 1 1 1
## 7 XANPAGTX0501_0… 0 0 1
## 8 XANPAGTX0501_0… 0 0 1
## 9 XANPAGTX0501_0… 0 0 1
## # ℹ abbreviated name: ¹`Apothecia / Vegetative (edge + center)`
- per functional group, how many of the lichen-upregulated genes are also apothecia-upregulated
lichen_upr<-read.delim2("../analysis_and_temp_files/08_dge_culture_lichen/upreg_in_lichen_sleuth.txt")
count_function<-ips_selected %>% filter(TranscriptID %in%lichen_upr$target_id) %>% group_by(Function) %>% summarize(total=n())
ips_selected %>% filter(TranscriptID %in% lichen_upr$target_id) %>%
mutate(is_ap = ifelse(TranscriptID %in% apothecia_up,T,F)) %>%
group_by(Function) %>% summarize(in_apothecia_up=sum(is_ap)) %>% left_join(count_function)
## Joining with `by = join_by(Function)`
## # A tibble: 19 × 3
## Function in_apothecia_up total
## <chr> <int> <int>
## 1 "Acetyl-CoA production and metabolism" 1 4
## 2 "Carbohydrate storage" 1 1
## 3 "Cell division, proliferation and growth" 6 12
## 4 "Cell surface and cell wall proteins" 2 9
## 5 "Cell wall biosynthesis " 1 1
## 6 "Cell wall misc" 0 2
## 7 "Cell wall remodeling" 1 3
## 8 "Defense" 1 3
## 9 "G-proteins and GPCR" 0 1
## 10 "Lipid metabolism" 0 3
## 11 "Oxylipins" 0 2
## 12 "Protein ubiquitination" 8 14
## 13 "RNA binding proteins" 4 5
## 14 "RNA interference" 3 3
## 15 "Ribosomal genes" 0 1
## 16 "Stress response genes" 0 1
## 17 "Transcription factors" 5 23
## 18 "Transporters" 0 27
## 19 "Velvet" 0 2
- None of lichen-upregulated transporters are apothecia-upregulated!
- Well, there is one protein we can id as a transporter that is upregulated in both, but in addition to that apothecia have 4 more that are not lichen upregulated!
compiled %>% filter(change=="apothecium", grepl("transporter",InterPro_new)) %>%
filter(InterPro_new!="IPR004853 Sugar phosphate transporter domain",
!grepl("ABC transporter-like",InterPro_new)) %>%
select(target_id,InterPro_new,b,Comparison) %>%
mutate(lichen_upregulated = ifelse(target_id %in%lichen_upr$target_id,T,F))
## # A tibble: 7 × 5
## target_id InterPro_new b Comparison lichen_upregulated
## <chr> <chr> <dbl> <chr> <lgl>
## 1 XANPAGTX0501_001825-T1 IPR003663 Sugar/in… -1.06 Apothecia… FALSE
## 2 XANPAGTX0501_010381-T1 IPR002293 Amino ac… -1.16 Apothecia… TRUE
## 3 XANPAGTX0501_008594-T1 IPR036259 MFS tran… -1.04 Edge / Ap… FALSE
## 4 XANPAGTX0501_000281-T1 IPR011701 Major fa… -1.28 Edge / Ap… FALSE
## 5 XANPAGTX0501_001825-T1 IPR003663 Sugar/in… -1.40 Edge / Ap… FALSE
## 6 XANPAGTX0501_009737-T1 IPR005829 Sugar tr… -1.54 Edge / Ap… FALSE
## 7 XANPAGTX0501_010381-T1 IPR002293 Amino ac… -1.59 Edge / Ap… TRUE
Of the tisuue-DGE genes, what portion was lichen/culture DGE?
culture_upr<-read.delim2("../analysis_and_temp_files/08_dge_culture_lichen/upreg_in_culture_sleuth.txt")
compiled %>% mutate(lichen_cult = case_when(
target_id %in% lichen_upr$target_id ~ "upreg_lichen" ,
target_id %in% culture_upr$target_id ~ "upreg_culture",
T ~ "non_dge"
)) %>% group_by(Comparison,change,lichen_cult) %>%
summarize(n=n()) %>%
pivot_wider(names_from=lichen_cult,values_from = n,values_fill = 0) %>%
mutate(total= upreg_lichen+upreg_culture+non_dge)
## `summarise()` has grouped output by 'Comparison', 'change'. You can override
## using the `.groups` argument.
## # A tibble: 7 × 6
## # Groups: Comparison, change [7]
## Comparison change non_dge upreg_culture upreg_lichen total
## <chr> <chr> <int> <int> <int> <int>
## 1 Apothecia / Vegetative (edge … apoth… 56 17 177 250
## 2 Apothecia / Vegetative (edge … thall… 0 1 1 2
## 3 Center / Apothecia apoth… 21 7 90 118
## 4 Center / Apothecia centre 0 0 1 1
## 5 Edge / Apothecia apoth… 121 25 225 371
## 6 Edge / Apothecia edge 3 1 9 13
## 7 Edge / Center centre 1 1 7 9
- look at the culture-upregulated genes
compiled2 <- compiled %>% mutate(lichen_cult = case_when(
target_id %in% lichen_upr$target_id ~ "upreg_lichen" ,
target_id %in% culture_upr$target_id ~ "upreg_culture",
T ~ "non_dge")) %>%
filter(lichen_cult=="upreg_culture")
compiled2 %>% kable(format = "html", col.names = colnames(compiled2)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "400px")
|
Comparison
|
change
|
target_id
|
b
|
InterPro_new
|
CAZyme_new
|
Protease_new
|
KO
|
secreted_consensus
|
lichen_ortho
|
lichen_cult
|
|
Apothecia / Vegetative (edge + center)
|
apothecium
|
XANPAGTX0501_007473-T1
|
-1.021407
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Apothecia / Vegetative (edge + center)
|
apothecium
|
XANPAGTX0501_001223-T1
|
-1.064214
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Apothecia / Vegetative (edge + center)
|
apothecium
|
XANPAGTX0501_009599-T1
|
-1.070929
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Apothecia / Vegetative (edge + center)
|
apothecium
|
XANPAGTX0501_001948-T1
|
-1.099351
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Apothecia / Vegetative (edge + center)
|
apothecium
|
XANPAGTX0501_006310-T1
|
-1.105045
|
IPR022137 Zinc finger protein, DUF3669 domain
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Apothecia / Vegetative (edge + center)
|
apothecium
|
XANPAGTX0501_001643-T1
|
-1.215746
|
IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily, IPR036047 F-box-like domain superfamily
|
NA
|
NA
|
|
FALSE
|
TRUE
|
upreg_culture
|
|
Apothecia / Vegetative (edge + center)
|
apothecium
|
XANPAGTX0501_001952-T1
|
-1.257146
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Apothecia / Vegetative (edge + center)
|
apothecium
|
XANPAGTX0501_001950-T1
|
-1.259001
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Apothecia / Vegetative (edge + center)
|
apothecium
|
XANPAGTX0501_001951-T1
|
-1.262779
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Apothecia / Vegetative (edge + center)
|
apothecium
|
XANPAGTX0501_001947-T1
|
-1.303157
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Apothecia / Vegetative (edge + center)
|
apothecium
|
XANPAGTX0501_002165-T1
|
-1.325802
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Apothecia / Vegetative (edge + center)
|
apothecium
|
XANPAGTX0501_002163-T1
|
-1.392989
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Apothecia / Vegetative (edge + center)
|
apothecium
|
XANPAGTX0501_002164-T1
|
-1.582652
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Apothecia / Vegetative (edge + center)
|
apothecium
|
XANPAGTX0501_009619-T1
|
-1.640066
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Apothecia / Vegetative (edge + center)
|
apothecium
|
XANPAGTX0501_003209-T1
|
-1.709229
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Apothecia / Vegetative (edge + center)
|
apothecium
|
XANPAGTX0501_009602-T1
|
-1.777131
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Apothecia / Vegetative (edge + center)
|
apothecium
|
XANPAGTX0501_008109-T1
|
-2.159140
|
IPR004143 Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain
|
NA
|
NA
|
K03800
|
FALSE
|
FALSE
|
upreg_culture
|
|
Apothecia / Vegetative (edge + center)
|
thallus
|
XANPAGTX0501_009376-T1
|
2.496154
|
IPR043141 Ribosomal protein L10-like domain superfamily
|
NA
|
NA
|
K02864
|
FALSE
|
FALSE
|
upreg_culture
|
|
Center / Apothecia
|
apothecium
|
XANPAGTX0501_002163-T1
|
-1.035184
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Center / Apothecia
|
apothecium
|
XANPAGTX0501_001947-T1
|
-1.046488
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Center / Apothecia
|
apothecium
|
XANPAGTX0501_001951-T1
|
-1.118810
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Center / Apothecia
|
apothecium
|
XANPAGTX0501_003209-T1
|
-1.170208
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Center / Apothecia
|
apothecium
|
XANPAGTX0501_009602-T1
|
-1.212068
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Center / Apothecia
|
apothecium
|
XANPAGTX0501_009619-T1
|
-1.314627
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Center / Apothecia
|
apothecium
|
XANPAGTX0501_008109-T1
|
-2.657633
|
IPR004143 Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain
|
NA
|
NA
|
K03800
|
FALSE
|
FALSE
|
upreg_culture
|
|
Edge / Apothecia
|
apothecium
|
XANPAGTX0501_005583-T1
|
-1.079779
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Edge / Apothecia
|
apothecium
|
XANPAGTX0501_000885-T1
|
-1.108859
|
IPR036305 RGS domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Edge / Apothecia
|
apothecium
|
XANPAGTX0501_010011-T1
|
-1.134493
|
IPR036013 Band 7/SPFH domain superfamily
|
NA
|
NA
|
K07192
|
FALSE
|
FALSE
|
upreg_culture
|
|
Edge / Apothecia
|
apothecium
|
XANPAGTX0501_009812-T1
|
-1.143459
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Edge / Apothecia
|
apothecium
|
XANPAGTX0501_009785-T1
|
-1.191020
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Edge / Apothecia
|
apothecium
|
XANPAGTX0501_009599-T1
|
-1.242828
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Edge / Apothecia
|
apothecium
|
XANPAGTX0501_003864-T1
|
-1.363940
|
IPR009075 Acyl-CoA dehydrogenase/oxidase C-terminal, IPR009100 Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily, IPR013786 Acyl-CoA dehydrogenase/oxidase, N-terminal, IPR036250 Acyl-CoA dehydrogenase-like, C-terminal, IPR037069 Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Edge / Apothecia
|
apothecium
|
XANPAGTX0501_007473-T1
|
-1.375934
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Edge / Apothecia
|
apothecium
|
XANPAGTX0501_007936-T1
|
-1.379176
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Edge / Apothecia
|
apothecium
|
XANPAGTX0501_005640-T1
|
-1.380432
|
IPR013087 Zinc finger C2H2-type
|
NA
|
NA
|
|
FALSE
|
TRUE
|
upreg_culture
|
|
Edge / Apothecia
|
apothecium
|
XANPAGTX0501_009761-T1
|
-1.387848
|
IPR001283 Cysteine-rich secretory protein-related, IPR014044 CAP domain, IPR018244 Allergen V5/Tpx-1-related, conserved site, IPR034120 None, IPR035940 CAP superfamily
|
NA
|
NA
|
K20412
|
TRUE
|
FALSE
|
upreg_culture
|
|
Edge / Apothecia
|
apothecium
|
XANPAGTX0501_001951-T1
|
-1.498238
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Edge / Apothecia
|
apothecium
|
XANPAGTX0501_009737-T1
|
-1.540774
|
IPR005829 Sugar transporter, conserved site, IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Edge / Apothecia
|
apothecium
|
XANPAGTX0501_001948-T1
|
-1.662753
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Edge / Apothecia
|
apothecium
|
XANPAGTX0501_001950-T1
|
-1.678963
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Edge / Apothecia
|
apothecium
|
XANPAGTX0501_001949-T1
|
-1.732732
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Edge / Apothecia
|
apothecium
|
XANPAGTX0501_001947-T1
|
-1.767840
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Edge / Apothecia
|
apothecium
|
XANPAGTX0501_002163-T1
|
-1.904022
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Edge / Apothecia
|
apothecium
|
XANPAGTX0501_001643-T1
|
-1.910689
|
IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily, IPR036047 F-box-like domain superfamily
|
NA
|
NA
|
|
FALSE
|
TRUE
|
upreg_culture
|
|
Edge / Apothecia
|
apothecium
|
XANPAGTX0501_002165-T1
|
-1.959472
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Edge / Apothecia
|
apothecium
|
XANPAGTX0501_001952-T1
|
-2.002699
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Edge / Apothecia
|
apothecium
|
XANPAGTX0501_009619-T1
|
-2.203533
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Edge / Apothecia
|
apothecium
|
XANPAGTX0501_003209-T1
|
-2.437600
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Edge / Apothecia
|
apothecium
|
XANPAGTX0501_009602-T1
|
-2.500879
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Edge / Apothecia
|
apothecium
|
XANPAGTX0501_002164-T1
|
-2.527734
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
|
Edge / Apothecia
|
edge
|
XANPAGTX0501_006869-T1
|
1.099929
|
IPR008979 Galactose-binding-like domain superfamily, IPR017853 Glycoside hydrolase superfamily, IPR024655 Asl1-like, glycosyl hydrolase catalytic domain
|
GH128
|
NA
|
|
TRUE
|
FALSE
|
upreg_culture
|
|
Edge / Center
|
centre
|
XANPAGTX0501_001949-T1
|
-1.187615
|
NA
|
NA
|
NA
|
|
FALSE
|
FALSE
|
upreg_culture
|
Visualize apothecia-upregulated genes in the genome
#list of upregulated genes
write.table(ap_a_genes$target_id,'../analysis_and_temp_files/09_dge_architecture/apothectia_upregulated.txt',col.names = F,row.names = F,quote = F)
#first half of the reference file: contig names and lengths
library(Biostrings)
## Loading required package: BiocGenerics
##
## Attaching package: 'BiocGenerics'
## The following objects are masked from 'package:lubridate':
##
## intersect, setdiff, union
## The following objects are masked from 'package:dplyr':
##
## combine, intersect, setdiff, union
## The following objects are masked from 'package:stats':
##
## IQR, mad, sd, var, xtabs
## The following objects are masked from 'package:base':
##
## anyDuplicated, append, as.data.frame, basename, cbind, colnames,
## dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
## grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
## order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
## rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
## union, unique, unsplit, which.max, which.min
## Loading required package: S4Vectors
## Warning: package 'S4Vectors' was built under R version 4.1.3
## Loading required package: stats4
##
## Attaching package: 'S4Vectors'
## The following objects are masked from 'package:lubridate':
##
## second, second<-
## The following objects are masked from 'package:dplyr':
##
## first, rename
## The following object is masked from 'package:tidyr':
##
## expand
## The following objects are masked from 'package:base':
##
## expand.grid, I, unname
## Loading required package: IRanges
##
## Attaching package: 'IRanges'
## The following object is masked from 'package:lubridate':
##
## %within%
## The following objects are masked from 'package:dplyr':
##
## collapse, desc, slice
## The following object is masked from 'package:purrr':
##
## reduce
## Loading required package: XVector
##
## Attaching package: 'XVector'
## The following object is masked from 'package:purrr':
##
## compact
## Loading required package: GenomeInfoDb
##
## Attaching package: 'Biostrings'
## The following object is masked from 'package:grid':
##
## pattern
## The following object is masked from 'package:base':
##
## strsplit
fasta<-readDNAStringSet("../../02_mycobiont_genome/analysis_and_temp_files/06_annotate_lecanoro/GTX0501_pred/annotate_results/Xanthoria_parietina_GTX0501.scaffolds.fa")
df<-data.frame("name"=names(fasta),"length"=width(fasta))
cat("## Chromosome lenghts\n",file='../analysis_and_temp_files/09_dge_architecture/reference.txt')
write.table(df,'../analysis_and_temp_files/09_dge_architecture/reference.txt',col.names = F,row.names = F,quote = F,append=T,sep="\t")
cat("\n", file="../analysis_and_temp_files/09_dge_architecture/reference.txt",append = T)
#second half of the reference file: gff
cat("## refGene\n",file='../analysis_and_temp_files/09_dge_architecture/reference.txt',append=T)
gff<-read.delim("../../02_mycobiont_genome/analysis_and_temp_files/06_annotate_lecanoro/GTX0501_pred/annotate_results/Xanthoria_parietina_GTX0501.gff3", header=F, comment.char="#")
gff2<-gff %>% filter(V3=="mRNA") %>%
mutate(target_id = str_match(V9,"ID=(.*);Parent")[,2]) %>%
select(target_id,V1,V4,V5)
gff2$name<- gff2$target_id
write.table(gff2,'../analysis_and_temp_files/09_dge_architecture/reference.txt',col.names = F,row.names = F,quote = F,append=T,sep="\t")
croc<-read.delim("../analysis_and_temp_files/09_dge_architecture/croc.txt",header=F)
croc$cluster<-paste0("cluster",1:nrow(croc))
croc<-croc %>% separate_longer_delim(V9, delim = " ") %>% filter(V9!="") %>%
select(-c(V7,V8,V2,V3))
colnames(croc)<-c("contig","start","end","pval","TranscriptID","cluster")
croc %>% group_by(cluster) %>% summarize(n=n()) %>% arrange(desc(n))
## # A tibble: 17 × 2
## cluster n
## <chr> <int>
## 1 cluster10 16
## 2 cluster12 10
## 3 cluster16 8
## 4 cluster2 5
## 5 cluster6 5
## 6 cluster14 4
## 7 cluster17 4
## 8 cluster1 3
## 9 cluster11 3
## 10 cluster13 3
## 11 cluster15 3
## 12 cluster3 3
## 13 cluster4 3
## 14 cluster5 3
## 15 cluster7 3
## 16 cluster8 3
## 17 cluster9 3
- Merge it with functional annotations and secreted status
croc2<-croc %>% left_join(funannot2) %>%
select(cluster,TranscriptID, InterPro_new,secreted_consensus)
## Joining with `by = join_by(TranscriptID)`
croc2 %>%
kable(format = "html", col.names = colnames(croc2)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "300px")
|
cluster
|
TranscriptID
|
InterPro_new
|
secreted_consensus
|
|
cluster1
|
XANPAGTX0501_000888-T1
|
NA
|
FALSE
|
|
cluster1
|
XANPAGTX0501_000892-T1
|
NA
|
FALSE
|
|
cluster1
|
XANPAGTX0501_000893-T1
|
NA
|
FALSE
|
|
cluster2
|
XANPAGTX0501_007871-T1
|
NA
|
FALSE
|
|
cluster2
|
XANPAGTX0501_007870-T1
|
NA
|
FALSE
|
|
cluster2
|
XANPAGTX0501_007872-T1
|
NA
|
FALSE
|
|
cluster2
|
XANPAGTX0501_007873-T1
|
NA
|
FALSE
|
|
cluster2
|
XANPAGTX0501_007869-T1
|
IPR000210 BTB/POZ domain, IPR011333 SKP1/BTB/POZ domain superfamily
|
FALSE
|
|
cluster3
|
XANPAGTX0501_008009-T1
|
NA
|
FALSE
|
|
cluster3
|
XANPAGTX0501_008008-T1
|
NA
|
FALSE
|
|
cluster3
|
XANPAGTX0501_008007-T1
|
NA
|
FALSE
|
|
cluster4
|
XANPAGTX0501_001061-T1
|
IPR002328 Alcohol dehydrogenase, zinc-type, conserved site, IPR011032 GroES-like superfamily, IPR013149 Alcohol dehydrogenase-like, C-terminal, IPR013154 Alcohol dehydrogenase-like, N-terminal, IPR020843 Polyketide synthase, enoylreductase domain, IPR036291 NAD(P)-binding domain superfamily
|
FALSE
|
|
cluster4
|
XANPAGTX0501_001064-T1
|
IPR021765 Mycotoxin biosynthesis protein UstYa-like
|
FALSE
|
|
cluster4
|
XANPAGTX0501_001063-T1
|
NA
|
TRUE
|
|
cluster5
|
XANPAGTX0501_001605-T1
|
NA
|
FALSE
|
|
cluster5
|
XANPAGTX0501_001611-T1
|
NA
|
FALSE
|
|
cluster5
|
XANPAGTX0501_001612-T1
|
NA
|
FALSE
|
|
cluster6
|
XANPAGTX0501_009326-T1
|
NA
|
FALSE
|
|
cluster6
|
XANPAGTX0501_009316-T1
|
IPR001810 F-box domain, IPR036047 F-box-like domain superfamily
|
FALSE
|
|
cluster6
|
XANPAGTX0501_009318-T1
|
IPR011333 SKP1/BTB/POZ domain superfamily
|
FALSE
|
|
cluster6
|
XANPAGTX0501_009321-T1
|
NA
|
FALSE
|
|
cluster6
|
XANPAGTX0501_009317-T1
|
IPR008979 Galactose-binding-like domain superfamily
|
TRUE
|
|
cluster7
|
XANPAGTX0501_009599-T1
|
NA
|
FALSE
|
|
cluster7
|
XANPAGTX0501_009602-T1
|
NA
|
FALSE
|
|
cluster7
|
XANPAGTX0501_009605-T1
|
NA
|
FALSE
|
|
cluster8
|
XANPAGTX0501_009621-T1
|
NA
|
FALSE
|
|
cluster8
|
XANPAGTX0501_009619-T1
|
NA
|
FALSE
|
|
cluster8
|
XANPAGTX0501_009615-T1
|
IPR035940 CAP superfamily
|
TRUE
|
|
cluster9
|
XANPAGTX0501_009786-T1
|
NA
|
FALSE
|
|
cluster9
|
XANPAGTX0501_009787-T1
|
NA
|
FALSE
|
|
cluster9
|
XANPAGTX0501_009795-T2
|
IPR023631 Amidase signature domain, IPR036928 Amidase signature (AS) superfamily
|
FALSE
|
|
cluster10
|
XANPAGTX0501_001964-T1
|
IPR001611 Leucine-rich repeat, IPR003591 Leucine-rich repeat, typical subtype, IPR019487 RAM signalling pathway, SOG2, IPR032675 Leucine-rich repeat domain superfamily
|
FALSE
|
|
cluster10
|
XANPAGTX0501_001960-T1
|
NA
|
FALSE
|
|
cluster10
|
XANPAGTX0501_001954-T1
|
NA
|
FALSE
|
|
cluster10
|
XANPAGTX0501_001951-T1
|
NA
|
FALSE
|
|
cluster10
|
XANPAGTX0501_001950-T1
|
NA
|
FALSE
|
|
cluster10
|
XANPAGTX0501_001947-T1
|
NA
|
FALSE
|
|
cluster10
|
XANPAGTX0501_001953-T1
|
NA
|
FALSE
|
|
cluster10
|
XANPAGTX0501_001948-T1
|
NA
|
FALSE
|
|
cluster10
|
XANPAGTX0501_001956-T1
|
NA
|
FALSE
|
|
cluster10
|
XANPAGTX0501_001963-T1
|
NA
|
FALSE
|
|
cluster10
|
XANPAGTX0501_001958-T1
|
IPR001356 Homeobox domain, IPR009057 Homeobox-like domain superfamily, IPR017970 Homeobox, conserved site
|
FALSE
|
|
cluster10
|
XANPAGTX0501_001962-T1
|
NA
|
FALSE
|
|
cluster10
|
XANPAGTX0501_001952-T1
|
NA
|
FALSE
|
|
cluster10
|
XANPAGTX0501_001967-T1
|
NA
|
FALSE
|
|
cluster10
|
XANPAGTX0501_001965-T1
|
NA
|
FALSE
|
|
cluster10
|
XANPAGTX0501_001955-T1
|
IPR001138 Zn(2)Cys(6) fungal-type DNA-binding domain, IPR001451 Hexapeptide repeat, IPR002110 Ankyrin repeat, IPR011004 Trimeric LpxA-like superfamily, IPR018357 Hexapeptide transferase, conserved site, IPR020683 Domain of unknown function DUF3447, IPR024688 Maltose/galactoside acetyltransferase, IPR036770 Ankyrin repeat-containing domain superfamily, IPR036864 Zn(2)-C6 fungal-type DNA-binding domain superfamily
|
FALSE
|
|
cluster11
|
XANPAGTX0501_002098-T1
|
IPR000504 RNA recognition motif domain, IPR012677 Nucleotide-binding alpha-beta plait domain superfamily, IPR035979 RNA-binding domain superfamily
|
FALSE
|
|
cluster11
|
XANPAGTX0501_002103-T1
|
IPR036910 High mobility group box domain superfamily
|
FALSE
|
|
cluster11
|
XANPAGTX0501_002104-T1
|
NA
|
FALSE
|
|
cluster12
|
XANPAGTX0501_002164-T1
|
NA
|
FALSE
|
|
cluster12
|
XANPAGTX0501_002185-T1
|
NA
|
FALSE
|
|
cluster12
|
XANPAGTX0501_002170-T1
|
NA
|
FALSE
|
|
cluster12
|
XANPAGTX0501_002182-T1
|
NA
|
FALSE
|
|
cluster12
|
XANPAGTX0501_002166-T1
|
NA
|
FALSE
|
|
cluster12
|
XANPAGTX0501_002163-T1
|
NA
|
FALSE
|
|
cluster12
|
XANPAGTX0501_002183-T1
|
NA
|
FALSE
|
|
cluster12
|
XANPAGTX0501_002172-T1
|
NA
|
FALSE
|
|
cluster12
|
XANPAGTX0501_002184-T1
|
NA
|
FALSE
|
|
cluster12
|
XANPAGTX0501_002165-T1
|
NA
|
FALSE
|
|
cluster13
|
XANPAGTX0501_010379-T1
|
NA
|
FALSE
|
|
cluster13
|
XANPAGTX0501_010380-T1
|
IPR000210 BTB/POZ domain, IPR011333 SKP1/BTB/POZ domain superfamily
|
FALSE
|
|
cluster13
|
XANPAGTX0501_010381-T1
|
IPR002293 Amino acid/polyamine transporter I
|
FALSE
|
|
cluster14
|
XANPAGTX0501_003211-T1
|
NA
|
FALSE
|
|
cluster14
|
XANPAGTX0501_003213-T1
|
IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily, IPR036047 F-box-like domain superfamily
|
FALSE
|
|
cluster14
|
XANPAGTX0501_003212-T1
|
IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily, IPR036047 F-box-like domain superfamily
|
FALSE
|
|
cluster14
|
XANPAGTX0501_003209-T1
|
NA
|
FALSE
|
|
cluster15
|
XANPAGTX0501_003765-T1
|
IPR000420 Yeast PIR protein repeat
|
TRUE
|
|
cluster15
|
XANPAGTX0501_003775-T1
|
IPR003100 PAZ domain, IPR003165 Piwi domain, IPR012337 Ribonuclease H-like superfamily, IPR014811 Argonaute, linker 1 domain, IPR032472 Argonaute linker 2 domain, IPR032473 Protein argonaute, Mid domain, IPR032474 Protein argonaute, N-terminal, IPR036085 PAZ domain superfamily, IPR036397 Ribonuclease H superfamily
|
FALSE
|
|
cluster15
|
XANPAGTX0501_003775-T2
|
IPR003100 PAZ domain, IPR003165 Piwi domain, IPR012337 Ribonuclease H-like superfamily, IPR014811 Argonaute, linker 1 domain, IPR032472 Argonaute linker 2 domain, IPR032473 Protein argonaute, Mid domain, IPR032474 Protein argonaute, N-terminal, IPR036085 PAZ domain superfamily, IPR036397 Ribonuclease H superfamily
|
FALSE
|
|
cluster16
|
XANPAGTX0501_005619-T1
|
NA
|
FALSE
|
|
cluster16
|
XANPAGTX0501_005613-T1
|
IPR003615 HNH nuclease
|
FALSE
|
|
cluster16
|
XANPAGTX0501_005614-T1
|
NA
|
FALSE
|
|
cluster16
|
XANPAGTX0501_005620-T1
|
IPR001841 Zinc finger, RING-type, IPR004331 SPX domain, IPR011016 Zinc finger, RING-CH-type, IPR013083 Zinc finger, RING/FYVE/PHD-type, IPR017907 Zinc finger, RING-type, conserved site
|
FALSE
|
|
cluster16
|
XANPAGTX0501_005615-T1
|
NA
|
FALSE
|
|
cluster16
|
XANPAGTX0501_005631-T1
|
IPR023631 Amidase signature domain, IPR036928 Amidase signature (AS) superfamily
|
FALSE
|
|
cluster16
|
XANPAGTX0501_005612-T1
|
NA
|
FALSE
|
|
cluster16
|
XANPAGTX0501_005630-T1
|
IPR036928 Amidase signature (AS) superfamily
|
FALSE
|
|
cluster17
|
XANPAGTX0501_006246-T1
|
NA
|
FALSE
|
|
cluster17
|
XANPAGTX0501_006255-T1
|
NA
|
FALSE
|
|
cluster17
|
XANPAGTX0501_006245-T1
|
NA
|
TRUE
|
|
cluster17
|
XANPAGTX0501_006253-T1
|
IPR014849 EKC/KEOPS complex, subunit Gon7
|
FALSE
|